Variant report

Variant	rs12298639
Chromosome Location	chr12:48136554-48136555
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	CTCF	chr12:48135649-48137339	A549	lung:	n/a	chr12:48136186-48136199 chr12:48136177-48136187 chr12:48136185-48136206 chr12:48136183-48136201
2	ZNF143	chr12:48136029-48136634	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr12:48136540-48136690	BJ	skin:	n/a	n/a
4	CBX3	chr12:48135971-48136680	K562	blood:	n/a	n/a
5	RAD21	chr12:48135868-48136702	ECC-1	luminal epithelium:	n/a	chr12:48136189-48136201 chr12:48136184-48136203 chr12:48136189-48136199 chr12:48136185-48136199 chr12:48136187-48136200
6	ZNF143	chr12:48136012-48136667	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr12:48136000-48136699	K562	blood:	n/a	n/a
8	SMC3	chr12:48134962-48137002	SK-N-SH	brain:	n/a	chr12:48136185-48136199
9	RAD21	chr12:48135624-48136619	HCT-116	colon:	n/a	chr12:48136189-48136201 chr12:48136184-48136203 chr12:48136189-48136199 chr12:48136185-48136199 chr12:48136187-48136200
10	ZNF143	chr12:48136000-48136675	GM12878	blood:	n/a	n/a
11	CTCF	chr12:48135150-48136817	SK-N-SH	brain:	n/a	chr12:48136186-48136199 chr12:48136177-48136187 chr12:48136185-48136206 chr12:48136183-48136201
12	RAD21	chr12:48135945-48136565	A549	lung:	n/a	chr12:48136189-48136201 chr12:48136184-48136203 chr12:48136189-48136199 chr12:48136185-48136199 chr12:48136187-48136200
13	RCOR1	chr12:48135967-48136716	K562	blood:	n/a	n/a
14	NR2F2	chr12:48135886-48136609	K562	blood:	n/a	n/a
15	MYC	chr12:48135953-48136717	NB4	blood:	n/a	n/a
16	POLR2A	chr12:48136429-48136566	HUVEC	blood vessel:	n/a	n/a
17	RAD21	chr12:48135829-48136582	A549	lung:	n/a	chr12:48136189-48136201 chr12:48136184-48136203 chr12:48136189-48136199 chr12:48136185-48136199 chr12:48136187-48136200
18	SMC3	chr12:48135938-48136607	Hela-S3	cervix:	n/a	chr12:48136185-48136199
19	RCOR1	chr12:48135989-48136555	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr12:48136520-48136670	HCFaa	heart:	n/a	n/a
21	CTCF	chr12:48135573-48136750	HCT-116	colon:	n/a	chr12:48136186-48136199 chr12:48136177-48136187 chr12:48136185-48136206 chr12:48136183-48136201
22	POLR2A	chr12:48136033-48136656	ECC-1	luminal epithelium:	n/a	n/a
23	CTCF	chr12:48136540-48136690	GM12873	blood:	n/a	n/a
24	RAD21	chr12:48134688-48138386	SK-N-SH	brain:	n/a	chr12:48137969-48137978 chr12:48136189-48136201 chr12:48136184-48136203 chr12:48137970-48137982 chr12:48136189-48136199 chr12:48136185-48136199 chr12:48137965-48137984 chr12:48136187-48136200 chr12:48137968-48137981
25	RAD21	chr12:48135814-48136773	HCT-116	colon:	n/a	chr12:48136189-48136201 chr12:48136184-48136203 chr12:48136189-48136199 chr12:48136185-48136199 chr12:48136187-48136200

No.	Distal block	Cell Line	Cell type
1	chr12:48135903..48138754-chr12:48165575..48168395,4	MCF-7	breast:
2	chr12:48111612..48114264-chr12:48135856..48138068,2	K562	blood:
3	chr12:48134835..48139182-chr12:48152118..48155732,5	MCF-7	breast:
4	chr12:48135112..48136657-chr12:48212167..48214385,2	K562	blood:
5	chr12:48136388..48139799-chr12:48164464..48168424,4	K562	blood:
6	chr12:48128880..48137705-chr12:48169546..48175532,12	K562	blood:
7	chr12:48135569..48136676-chr12:48166473..48167804,4	MCF-7	breast:
8	chr12:48111014..48111901-chr12:48135670..48136730,5	MCF-7	breast:
9	chr12:48135061..48136993-chr12:48147045..48149552,2	MCF-7	breast:
10	chr12:48116790..48119550-chr12:48135315..48137472,2	K562	blood:
11	chr12:48136219..48136843-chr12:48172879..48173592,2	MCF-7	breast:
12	chr12:48099217..48102022-chr12:48134946..48137757,2	K562	blood:
13	chr12:48136182..48136821-chr12:48160641..48161512,4	K562	blood:
14	chr12:48131407..48141823-chr12:48163910..48172152,16	MCF-7	breast:

Variant related genes	Relation type
RAPGEF3	TF binding region
ENSG00000005175	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000111405	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs7308119	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs877196	0.91[YRI][hapmap]
rs877197	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:48129200-48137600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:48129400-48138600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:48129800-48137600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:48130000-48146000	Weak transcription	Small Intestine	intestine
7	chr12:48130400-48137600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:48130600-48138800	Weak transcription	Fetal Intestine Large	intestine
9	chr12:48131000-48143000	Weak transcription	Aorta	Aorta
10	chr12:48131200-48141600	Weak transcription	Fetal Kidney	kidney
11	chr12:48131200-48145600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:48131600-48136600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr12:48131800-48141000	Weak transcription	Gastric	stomach
14	chr12:48132400-48146600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:48132800-48136600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr12:48133600-48136600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:48133600-48136600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:48133600-48136600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:48133600-48137000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr12:48134000-48136600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:48134000-48136600	Enhancers	Brain Anterior Caudate	brain
22	chr12:48134400-48137000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr12:48134400-48138600	Weak transcription	K562	blood
24	chr12:48134600-48136600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:48134800-48136600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr12:48134800-48136600	Enhancers	Stomach Mucosa	stomach
27	chr12:48134800-48136600	Enhancers	Dnd41	blood
28	chr12:48134800-48147000	Weak transcription	Psoas Muscle	Psoas
29	chr12:48135000-48137600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:48135000-48138200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:48135000-48145400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:48135200-48138600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:48135200-48140200	Weak transcription	Fetal Intestine Small	intestine
34	chr12:48135400-48137000	Weak transcription	Fetal Stomach	stomach
35	chr12:48135400-48137200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:48135400-48137400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:48135400-48137400	Weak transcription	Hela-S3	cervix
38	chr12:48135400-48139000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:48135400-48139800	Weak transcription	Ovary	ovary
40	chr12:48135400-48147000	Weak transcription	Colonic Mucosa	Colon
41	chr12:48135400-48147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:48135600-48137400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:48135600-48137600	Weak transcription	Pancreas	Pancrea
44	chr12:48135600-48137600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr12:48135600-48137600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:48135600-48138200	Weak transcription	Brain Germinal Matrix	brain
47	chr12:48135600-48138800	Weak transcription	Fetal Lung	lung
48	chr12:48135600-48138800	Weak transcription	Right Atrium	heart
49	chr12:48135600-48139600	Weak transcription	Lung	lung
50	chr12:48135600-48140400	Weak transcription	Esophagus	oesophagus

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