Variant report

Variant	rs7309871
Chromosome Location	chr12:12681550-12681551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12676963..12678914-chr12:12679102..12682035,2	MCF-7	breast:
2	chr12:12673672..12675472-chr12:12680343..12682514,2	MCF-7	breast:
3	chr12:12673839..12677511-chr12:12678935..12682743,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10845573	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11054950	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11054960	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054961	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054965	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12308450	0.93[AMR][1000 genomes]
rs12309782	0.93[AMR][1000 genomes]
rs12309848	0.93[AMR][1000 genomes]
rs4421828	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58968872	0.93[AMR][1000 genomes]
rs7138733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7295113	0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv523022	chr12:12673551-12688181	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
2	chr12:12641600-12686200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:12660000-12681800	Weak transcription	Fetal Kidney	kidney
4	chr12:12660400-12686200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:12664000-12690400	Weak transcription	NHLF	lung
6	chr12:12665000-12684400	Weak transcription	NHDF-Ad	bronchial
7	chr12:12665000-12685600	Weak transcription	HMEC	breast
8	chr12:12665000-12686200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:12667400-12686400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:12671400-12686200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:12671400-12686200	Weak transcription	Fetal Stomach	stomach
12	chr12:12672800-12691200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:12673000-12685200	Weak transcription	NHEK	skin
14	chr12:12673000-12690200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:12673200-12682600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:12674200-12691200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:12674400-12682000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:12674400-12683000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:12674400-12685600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:12674600-12686200	Weak transcription	NH-A	brain
21	chr12:12677200-12686200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:12677400-12686200	Weak transcription	Brain Angular Gyrus	brain
23	chr12:12677400-12686200	Weak transcription	Brain Anterior Caudate	brain
24	chr12:12677400-12686200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:12677600-12686200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:12678400-12683000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:12678600-12682000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:12678600-12682400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr12:12678600-12683400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:12679000-12682400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:12679400-12681600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr12:12679400-12681600	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr12:12679400-12682200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr12:12679400-12682200	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr12:12679400-12682400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr12:12679400-12682600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr12:12679400-12683000	Enhancers	Primary T cells from cord blood	blood
38	chr12:12679400-12683800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:12679600-12681800	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr12:12679600-12682200	Enhancers	Primary T cells fromperipheralblood	blood
41	chr12:12679600-12682400	Genic enhancers	Fetal Intestine Small	intestine
42	chr12:12679600-12682600	Enhancers	Stomach Mucosa	stomach
43	chr12:12679600-12683600	Enhancers	Fetal Intestine Large	intestine
44	chr12:12679600-12686400	Enhancers	Fetal Heart	heart
45	chr12:12679800-12683400	Enhancers	Duodenum Mucosa	Duodenum
46	chr12:12679800-12683600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr12:12680000-12686800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:12680200-12681600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr12:12680200-12683400	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr12:12680200-12686200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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