Variant report

Variant	rs35241668
Chromosome Location	chr12:497993-497994
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	TAF1	chr12:497917-498680	GM12892	blood:	n/a	n/a
2	CTCF	chr12:497900-498050	Caco-2	colon:	n/a	n/a
3	MYC	chr12:497716-499110	NB4	blood:	n/a	n/a
4	YY1	chr12:497862-498848	H1-hESC	embryonic stem cell:	n/a	n/a
5	CHD1	chr12:496627-499304	IMR90	lung:	n/a	n/a
6	POLR2A	chr12:497918-499065	GM18951	blood:	n/a	n/a
7	ELF1	chr12:497989-499205	HCT-116	colon:	n/a	n/a
8	POLR2A	chr12:497660-499115	GM12878	blood:	n/a	n/a
9	GABPA	chr12:497941-499291	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr12:497941-499069	K562	blood:	n/a	n/a
11	POLR2A	chr12:497739-499255	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:497758-499038	GM12878	blood:	n/a	n/a
13	YY1	chr12:497968-498667	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:497742-499133	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:497790-499064	GM15510	blood:	n/a	n/a
16	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
17	POLR2A	chr12:497960-499333	NB4	blood:	n/a	n/a
18	POLR2A	chr12:497794-499127	GM19193	blood:	n/a	n/a
19	POLR2A	chr12:497947-499299	GM12891	blood:	n/a	n/a
20	GATA1	chr12:496989-498110	PBDE	blood:	n/a	chr12:497068-497089 chr12:497428-497436
21	PML	chr12:497985-499257	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:497500-500023	H1-hESC	embryonic stem cell:	n/a	n/a
23	REST	chr12:497968-499138	HL-60	blood:	n/a	n/a
24	POLR2A	chr12:497685-499277	H1-neurons	neurons:	n/a	n/a
25	MAFK	chr12:497918-499187	Hela-S3	cervix:	n/a	n/a
26	SIN3A	chr12:497715-499093	GM12878	blood:	n/a	n/a
27	CREB1	chr12:497901-499203	HepG2	liver:	n/a	n/a
28	FOXM1	chr12:497963-499092	GM12878	blood:	n/a	n/a
29	MAZ	chr12:497856-499164	IMR90	lung:	n/a	n/a
30	POLR2A	chr12:497504-499232	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr12:497912-499498	Hela-S3	cervix:	n/a	n/a
32	MAZ	chr12:497677-499186	GM12878	blood:	n/a	n/a
33	REST	chr12:497539-499633	H1-neurons	neurons:	n/a	n/a
34	TCF12	chr12:497730-499238	ECC-1	luminal epithelium:	n/a	n/a
35	MAX	chr12:497970-499020	GM12878	blood:	n/a	n/a
36	POLR2A	chr12:497941-499208	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr12:497602-499299	GM12878	blood:	n/a	n/a
38	CHD2	chr12:497976-499158	H1-hESC	embryonic stem cell:	n/a	n/a
39	CHD2	chr12:497751-499018	Hela-S3	cervix:	n/a	n/a
40	STAT5A	chr12:497651-499130	GM12878	blood:	n/a	chr12:498658-498670 chr12:498268-498280 chr12:498270-498282 chr12:498269-498281
41	POLR2A	chr12:497828-499277	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr12:497988-499491	ECC-1	luminal epithelium:	n/a	n/a
43	GABPA	chr12:497634-499309	A549	lung:	n/a	n/a
44	POLR2A	chr12:497502-499281	GM12878	blood:	n/a	n/a
45	ZBTB7A	chr12:497922-499134	ECC-1	luminal epithelium:	n/a	n/a
46	BCLAF1	chr12:497860-499069	GM12878	blood:	n/a	chr12:498781-498790 chr12:498492-498501
47	CHD1	chr12:497953-499557	H1-hESC	embryonic stem cell:	n/a	n/a
48	MXI1	chr12:497605-499362	GM12878	blood:	n/a	n/a
49	GABPA	chr12:497885-499326	SK-N-SH	brain:	n/a	n/a
50	MAZ	chr12:497938-499025	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:497611..500419-chr12:508788..511712,2	MCF-7	breast:
2	chr12:496401..500895-chr12:509695..513736,6	K562	blood:
3	chr12:418157..420807-chr12:497062..498857,2	MCF-7	breast:

Variant related genes	Relation type
KDM5A	TF binding region
CCDC77	TF binding region
ENSG00000073614	Chromatin interaction
ENSG00000120647	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12582581	0.81[EUR][1000 genomes]
rs34197179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34905395	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35171949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58498459	0.81[EUR][1000 genomes]
rs7138499	0.81[EUR][1000 genomes]
rs7313676	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 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

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	chr12:495400-498000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr12:495600-498000	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr12:495600-499400	Active TSS	K562	blood
6	chr12:495600-499600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr12:495600-499800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:495800-499000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:495800-499200	Active TSS	A549	lung
10	chr12:495800-499600	Active TSS	Right Atrium	heart
11	chr12:496000-499000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:496000-499000	Active TSS	HMEC	breast
13	chr12:496000-499000	Active TSS	HSMM	muscle
14	chr12:496000-499400	Active TSS	Thymus	Thymus
15	chr12:496000-499400	Active TSS	NHLF	lung
16	chr12:496000-499600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:496200-499000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:496200-499000	Active TSS	Fetal Intestine Large	intestine
19	chr12:496200-499200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr12:496200-499400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr12:496200-499400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:496200-499400	Active TSS	NHDF-Ad	bronchial
23	chr12:496400-498000	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr12:496400-499000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:496400-499000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:496400-499000	Active TSS	Hela-S3	cervix
27	chr12:496400-499000	Active TSS	HSMMtube	muscle
28	chr12:496400-499400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:496400-499400	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr12:496400-499400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr12:496400-499800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:496600-498000	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr12:496600-498000	Flanking Active TSS	Liver	Liver
34	chr12:496600-498200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:496600-499000	Active TSS	Primary T cells fromperipheralblood	blood
36	chr12:496600-499000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:496600-499000	Active TSS	Fetal Muscle Leg	muscle
38	chr12:496600-499000	Active TSS	Fetal Stomach	stomach
39	chr12:496600-499200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:496600-499200	Active TSS	Right Ventricle	heart
41	chr12:496600-499400	Active TSS	Fetal Intestine Small	intestine
42	chr12:496600-499400	Active TSS	Fetal Thymus	thymus
43	chr12:496600-499600	Active TSS	H1 Cell Line	embryonic stem cell
44	chr12:496800-498000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr12:496800-499000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:496800-499000	Active TSS	Colonic Mucosa	Colon
47	chr12:496800-499000	Active TSS	Placenta	Placenta
48	chr12:496800-499000	Active TSS	Left Ventricle	heart
49	chr12:496800-499200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr12:496800-499200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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