Variant report

Variant	rs12665952
Chromosome Location	chr7:116564260-116564261
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:116562487..116565467-chr7:116567653..116570595,2	MCF-7	breast:
2	chr7:116562838..116565216-chr7:116567059..116569364,3	K562	blood:
3	chr7:116563032..116565216-chr7:116567059..116570510,3	K562	blood:
4	7:115847372-115857098..7:116562887-116565888	H1-hESC	embryonic stem cell:	embryo
5	chr7:116555853..116558768-chr7:116563392..116564954,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135269	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10487354	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10487355	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10487356	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10953829	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10953830	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12533164	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12533755	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12669383	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12670056	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12670264	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12671827	0.93[EUR][1000 genomes]
rs12671828	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12672008	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12673979	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12674017	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12706108	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12706109	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12706110	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12706112	0.97[EUR][1000 genomes]
rs12706115	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12706120	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12706121	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12706122	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12706123	0.82[EUR][1000 genomes]
rs13222845	0.93[EUR][1000 genomes]
rs13224082	0.95[EUR][1000 genomes]
rs13228847	0.96[EUR][1000 genomes]
rs13239000	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237720	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2299441	0.94[EUR][1000 genomes]
rs2301649	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3173936	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3807999	0.95[EUR][1000 genomes]
rs4808	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7808129	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9791492	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9791721	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][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	nsv831107	chr7:116414734-116649466	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv889074	chr7:116552859-116604194	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv889075	chr7:116552859-116610237	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv889073	chr7:116552859-116611113	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116544000-116568600	Weak transcription	Fetal Brain Male	brain
2	chr7:116544400-116570600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:116552000-116570600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:116552400-116569000	Weak transcription	NHLF	lung
5	chr7:116553200-116570600	Weak transcription	Brain Substantia Nigra	brain
6	chr7:116555400-116568800	Weak transcription	Gastric	stomach
7	chr7:116555400-116570400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:116556800-116570600	Weak transcription	Aorta	Aorta
9	chr7:116557000-116565000	Weak transcription	Left Ventricle	heart
10	chr7:116557000-116570800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:116557000-116570800	Weak transcription	NHEK	skin
12	chr7:116558000-116565400	Weak transcription	Fetal Stomach	stomach
13	chr7:116558000-116565800	Weak transcription	Fetal Muscle Leg	muscle
14	chr7:116558000-116567600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:116558000-116570600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr7:116558000-116570600	Weak transcription	Lung	lung
17	chr7:116558000-116570800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:116558200-116570400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr7:116558200-116570400	Weak transcription	Brain Hippocampus Middle	brain
20	chr7:116558200-116570600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr7:116558200-116570800	Weak transcription	HMEC	breast
22	chr7:116558400-116564600	Weak transcription	NH-A	brain
23	chr7:116558400-116564800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr7:116558400-116568400	Weak transcription	HepG2	liver
25	chr7:116558400-116570600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:116558400-116570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:116558400-116570600	Weak transcription	Brain Anterior Caudate	brain
28	chr7:116558400-116570800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:116558600-116570400	Weak transcription	Fetal Lung	lung
30	chr7:116558600-116570600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr7:116558800-116570400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:116558800-116570400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr7:116559000-116565400	Weak transcription	K562	blood
34	chr7:116559000-116567600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:116559000-116570200	Weak transcription	Placenta	Placenta
36	chr7:116559000-116570400	Weak transcription	Dnd41	blood
37	chr7:116559000-116570400	Weak transcription	Hela-S3	cervix
38	chr7:116559200-116564400	Weak transcription	Osteobl	bone
39	chr7:116559200-116567400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr7:116559200-116567600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:116559200-116570600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:116559200-116570600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:116559200-116570600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:116559200-116576000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr7:116559400-116567800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr7:116559600-116565200	Weak transcription	HSMM	muscle
47	chr7:116559600-116567400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr7:116559600-116570400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr7:116559600-116570400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr7:116559600-116570600	Weak transcription	GM12878-XiMat	blood

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