Variant report

Variant	rs2401385
Chromosome Location	chr12:9799126-9799127
allele	A/G
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	POLR2A	chr12:9794253-9800349	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9786143..9793024-chr12:9797652..9803573,13	MCF-7	breast:
2	chr12:9522809..9525392-chr12:9798242..9800347,2	K562	blood:
3	chr12:9794237..9796835-chr12:9798704..9800341,2	MCF-7	breast:
4	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:
5	chr12:9785588..9787603-chr12:9798282..9800898,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256594	TF binding region
ENSG00000272917	Chromatin interaction
ENSG00000256594	Chromatin interaction
ENSG00000233719	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10047657	0.82[CEU][hapmap]
rs10772001	0.82[CEU][hapmap]
rs10844269	0.86[EUR][1000 genomes]
rs11052384	0.82[YRI][hapmap]
rs1863873	0.86[CEU][hapmap]
rs2401386	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7132715	0.86[EUR][1000 genomes]

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	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9771600-9799200	Weak transcription	Fetal Lung	lung
2	chr12:9785400-9799400	Weak transcription	Fetal Brain Male	brain
3	chr12:9787400-9799800	Weak transcription	Pancreas	Pancrea
4	chr12:9791600-9799400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:9792000-9800000	Weak transcription	NHEK	skin
6	chr12:9792600-9800000	Weak transcription	Brain Germinal Matrix	brain
7	chr12:9792800-9800200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:9793000-9800000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:9794400-9800200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:9795000-9799600	Enhancers	Primary T cells from cord blood	blood
11	chr12:9795200-9799600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr12:9795200-9799600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr12:9795200-9799600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:9795600-9799800	Weak transcription	Fetal Stomach	stomach
15	chr12:9795800-9800200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:9796000-9799800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:9796400-9799400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:9796400-9799600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:9796400-9799800	Weak transcription	Thymus	Thymus
20	chr12:9796600-9799400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr12:9796600-9799400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:9796600-9799400	Weak transcription	Fetal Thymus	thymus
23	chr12:9796600-9800200	Weak transcription	Gastric	stomach
24	chr12:9797600-9799400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:9797800-9799600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:9797800-9799800	Weak transcription	Hela-S3	cervix
27	chr12:9797800-9800000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:9798000-9799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:9798000-9799400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:9798200-9799400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr12:9798200-9799800	Weak transcription	HMEC	breast
32	chr12:9798200-9800000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr12:9798400-9799600	Weak transcription	A549	lung
34	chr12:9798600-9799400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:9798600-9799400	Enhancers	GM12878-XiMat	blood
36	chr12:9798600-9800000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:9798800-9799800	Weak transcription	Stomach Mucosa	stomach
38	chr12:9798800-9800200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr12:9798800-9800200	Enhancers	HUVEC	blood vessel
40	chr12:9799000-9799400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr12:9799000-9799800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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