Variant report

Variant	rs7306393
Chromosome Location	chr12:499041-499042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr12:498156-499343	H1-neurons	neurons:	n/a	n/a
2	SP1	chr12:498023-499192	A549	lung:	n/a	chr12:498491-498502 chr12:498491-498503 chr12:498491-498503 chr12:498662-498671 chr12:498274-498283 chr12:498492-498506 chr12:498658-498672 chr12:498663-498672 chr12:498493-498502
3	TAF1	chr12:498715-499104	Hela-S3	cervix:	n/a	n/a
4	GABPA	chr12:498008-499143	K562	blood:	n/a	n/a
5	SIN3AK20	chr12:498709-499101	A549	lung:	n/a	n/a
6	MYC	chr12:497716-499110	NB4	blood:	n/a	n/a
7	POLR2A	chr12:498202-499061	GM10847	blood:	n/a	n/a
8	POLR2A	chr12:498016-499219	H1-neurons	neurons:	n/a	n/a
9	MYC	chr12:498097-499083	K562	blood:	n/a	n/a
10	USF2	chr12:498423-499055	H1-hESC	embryonic stem cell:	n/a	chr12:498491-498507
11	TBP	chr12:498021-499047	K562	blood:	n/a	n/a
12	POLR2A	chr12:498169-499063	Gliobla	brain:	n/a	n/a
13	MAX	chr12:498321-499081	H1-hESC	embryonic stem cell:	n/a	n/a
14	CHD1	chr12:496627-499304	IMR90	lung:	n/a	n/a
15	SRF	chr12:498227-499208	MCF-7	breast:	n/a	n/a
16	BRCA1	chr12:498301-499078	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr12:497918-499065	GM18951	blood:	n/a	n/a
18	TEAD4	chr12:498260-499108	ECC-1	luminal epithelium:	n/a	chr12:498787-498796
19	ELF1	chr12:497989-499205	HCT-116	colon:	n/a	n/a
20	BCL3	chr12:498186-499130	A549	lung:	n/a	chr12:498781-498790 chr12:498492-498501
21	POLR2A	chr12:497660-499115	GM12878	blood:	n/a	n/a
22	GABPA	chr12:497941-499291	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr12:497941-499069	K562	blood:	n/a	n/a
24	NFIC	chr12:498286-499115	HepG2	liver:	n/a	n/a
25	POLR2A	chr12:497739-499255	HepG2	liver:	n/a	n/a
26	PML	chr12:498237-499143	K562	blood:	n/a	n/a
27	MAX	chr12:497995-499095	HepG2	liver:	n/a	n/a
28	HCFC1	chr12:498299-499158	K562	blood:	n/a	n/a
29	POLR2A	chr12:497742-499133	Hela-S3	cervix:	n/a	n/a
30	SRF	chr12:498447-499064	MCF-7	breast:	n/a	n/a
31	POLR2A	chr12:497790-499064	GM15510	blood:	n/a	n/a
32	TBL1XR1	chr12:498160-499057	K562	blood:	n/a	n/a
33	ETS1	chr12:497921-499150	A549	lung:	n/a	chr12:498466-498475 chr12:498821-498830 chr12:498813-498830 chr12:498269-498280 chr12:498818-498833 chr12:498401-498412 chr12:498821-498830 chr12:498401-498414 chr12:498821-498830 chr12:498268-498279 chr12:498821-498830 chr12:498818-498834 chr12:498493-498504 chr12:498271-498282 chr12:498820-498833 chr12:498813-498830 chr12:498466-498475 chr12:498266-498277 chr12:498776-498785 chr12:498267-498278 chr12:498821-498830 chr12:498272-498285 chr12:498467-498477 chr12:498270-498281 chr12:498821-498830
34	TCF7L2	chr12:498271-499088	HCT-116	colon:	n/a	chr12:498989-498996
35	POLR2A	chr12:497960-499333	NB4	blood:	n/a	n/a
36	POLR2A	chr12:497794-499127	GM19193	blood:	n/a	n/a
37	POLR2A	chr12:497947-499299	GM12891	blood:	n/a	n/a
38	POLR2A	chr12:498144-499091	HEK293	kidney:	n/a	n/a
39	NRF1	chr12:498430-499092	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:498136-499150	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr12:498034-499271	HL-60	blood:	n/a	n/a
42	MAX	chr12:498032-499151	HepG2	liver:	n/a	n/a
43	CREB1	chr12:498092-499250	H1-hESC	embryonic stem cell:	n/a	n/a
44	PML	chr12:497985-499257	GM12878	blood:	n/a	n/a
45	MAX	chr12:498232-499060	MCF-7	breast:	n/a	n/a
46	TAF7	chr12:498707-499176	H1-hESC	embryonic stem cell:	n/a	n/a
47	MYC	chr12:498137-499225	K562	blood:	n/a	n/a
48	POLR2A	chr12:498100-499079	HepG2	liver:	n/a	n/a
49	POLR2A	chr12:498057-499085	K562	blood:	n/a	n/a
50	RCOR1	chr12:498215-499100	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:10002901..10003432-chr12:498459..499050,2	Hela-S3	cervix:
2	chr12:497611..500419-chr12:508788..511712,2	MCF-7	breast:
3	chr12:496401..500895-chr12:509695..513736,6	K562	blood:
4	chr12:498804..500777-chr12:509921..512244,2	K562	blood:
5	chr12:498195..499241-chr14:91294171..91295172,4	Hela-S3	cervix:
6	chr12:498060..499050-chr5:131892887..131893550,2	Hela-S3	cervix:

Variant related genes	Relation type
KDM5A	TF binding region
ENSG00000113522	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000120647	Chromatin interaction
ENSG00000258884	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs56288640	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60979935	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61103141	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7313676	1.00[MEX][hapmap]
rs74055609	1.00[AMR][1000 genomes]
rs7957592	1.00[AMR][1000 genomes]
rs7979991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs956231	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051726	chr12:282465-511843	Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541304	chr12:282465-635505	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1042991	chr12:282465-666255	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1041574	chr12:282465-812000	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv1050781	chr12:321353-783899	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv1040849	chr12:321619-771493	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv541322	chr12:321619-771493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv1035679	chr12:321619-781558	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv1053519	chr12:321619-828175	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
14	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
15	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
16	esv2757484	chr12:335010-543206	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	esv2759875	chr12:335010-990544	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
18	nsv1045638	chr12:349031-893536	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
19	nsv541325	chr12:349031-893536	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
20	nsv1050646	chr12:362398-658665	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
21	nsv541326	chr12:362398-658665	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
22	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
23	nsv898565	chr12:428131-564185	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
24	nsv1052201	chr12:429128-515675	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
25	nsv541328	chr12:429128-515675	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
26	nsv442250	chr12:432808-543847	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	esv2756520	chr12:433151-543206	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
28	nsv1050226	chr12:441032-743195	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
29	nsv1035222	chr12:449993-515675	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
30	esv2758290	chr12:457433-990544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
31	nsv949226	chr12:493900-814882	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
32	nsv898566	chr12:499041-570917	Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:494800-499600	Active TSS	GM12878-XiMat	blood
2	chr12:495000-499400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:495600-499400	Active TSS	K562	blood
4	chr12:495600-499600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr12:495600-499800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:495800-499200	Active TSS	A549	lung
7	chr12:495800-499600	Active TSS	Right Atrium	heart
8	chr12:496000-499400	Active TSS	Thymus	Thymus
9	chr12:496000-499400	Active TSS	NHLF	lung
10	chr12:496000-499600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:496200-499200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr12:496200-499400	Active TSS	Muscle Satellite Cultured Cells	--
13	chr12:496200-499400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:496200-499400	Active TSS	NHDF-Ad	bronchial
15	chr12:496400-499400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:496400-499400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr12:496400-499400	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr12:496400-499800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:496600-499200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:496600-499200	Active TSS	Right Ventricle	heart
21	chr12:496600-499400	Active TSS	Fetal Intestine Small	intestine
22	chr12:496600-499400	Active TSS	Fetal Thymus	thymus
23	chr12:496600-499600	Active TSS	H1 Cell Line	embryonic stem cell
24	chr12:496800-499200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr12:496800-499200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:496800-499200	Active TSS	Aorta	Aorta
27	chr12:496800-499200	Active TSS	Fetal Brain Male	brain
28	chr12:496800-499200	Active TSS	Ovary	ovary
29	chr12:496800-499200	Bivalent/Poised TSS	HepG2	liver
30	chr12:496800-499400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:496800-499400	Active TSS	Fetal Kidney	kidney
32	chr12:496800-499400	Active TSS	Fetal Muscle Trunk	muscle
33	chr12:496800-499400	Active TSS	Osteobl	bone
34	chr12:497000-499200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:497000-499200	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr12:497000-499200	Active TSS	Esophagus	oesophagus
37	chr12:497000-499200	Active TSS	Lung	lung
38	chr12:497000-499200	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr12:497000-499200	Active TSS	Stomach Mucosa	stomach
40	chr12:497000-499400	Active TSS	H9 Cell Line	embryonic stem cell
41	chr12:497000-499400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:497000-499600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:497200-499200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:497200-499200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:497200-499200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:497200-499200	Active TSS	Gastric	stomach
47	chr12:497200-499400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr12:497200-499400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:497200-499600	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr12:497200-499800	Active TSS	HUES64 Cell Line	embryonic stem cell

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