Variant report

Variant	rs12706121
Chromosome Location	chr7:116562288-116562289
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:115890993-115892266..7:116559477-116562887	H1-hESC	embryonic stem cell:	embryo
2	7:115847372-115857098..7:116559477-116562887	GM12878	blood:
3	7:116559477-116562887..7:116754962-116765597	GM12878	blood:
4	7:115861595-115870968..7:116559477-116562887	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000004866	Chromatin interaction
ENSG00000135269	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10487354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10487355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10487356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10953830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953831	0.80[TSI][hapmap]
rs12533164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12533755	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665952	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12669383	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12670056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12670264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12671827	0.94[EUR][1000 genomes]
rs12671828	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12672008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12673979	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12674017	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12706108	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12706109	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12706110	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12706112	0.99[EUR][1000 genomes]
rs12706115	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12706120	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12706122	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12706123	0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs13222845	0.94[EUR][1000 genomes]
rs13224082	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13228847	0.97[EUR][1000 genomes]
rs13239000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237720	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2299441	0.95[EUR][1000 genomes]
rs2301649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3173936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3807999	0.88[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs4808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804651	0.85[TSI][hapmap]
rs7808129	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9791492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9791721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116538200-116562400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr7:116543200-116562400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr7:116544000-116568600	Weak transcription	Fetal Brain Male	brain
4	chr7:116544400-116570600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:116550000-116562400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:116552000-116570600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr7:116552400-116569000	Weak transcription	NHLF	lung
8	chr7:116553200-116570600	Weak transcription	Brain Substantia Nigra	brain
9	chr7:116553600-116563400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:116555200-116563200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:116555400-116562600	Weak transcription	Esophagus	oesophagus
12	chr7:116555400-116563200	Weak transcription	Pancreas	Pancrea
13	chr7:116555400-116568800	Weak transcription	Gastric	stomach
14	chr7:116555400-116570400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr7:116556400-116562800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:116556800-116564200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:116556800-116570600	Weak transcription	Aorta	Aorta
18	chr7:116557000-116562800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr7:116557000-116565000	Weak transcription	Left Ventricle	heart
20	chr7:116557000-116570800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:116557000-116570800	Weak transcription	NHEK	skin
22	chr7:116557600-116562400	Weak transcription	Fetal Intestine Small	intestine
23	chr7:116558000-116562400	Weak transcription	Psoas Muscle	Psoas
24	chr7:116558000-116562800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr7:116558000-116563000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr7:116558000-116564000	Weak transcription	Thymus	Thymus
27	chr7:116558000-116565400	Weak transcription	Fetal Stomach	stomach
28	chr7:116558000-116565800	Weak transcription	Fetal Muscle Leg	muscle
29	chr7:116558000-116567600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr7:116558000-116570600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr7:116558000-116570600	Weak transcription	Lung	lung
32	chr7:116558000-116570800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:116558200-116562400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:116558200-116562800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr7:116558200-116570400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:116558200-116570400	Weak transcription	Brain Hippocampus Middle	brain
37	chr7:116558200-116570600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr7:116558200-116570800	Weak transcription	HMEC	breast
39	chr7:116558400-116564000	Weak transcription	Brain Angular Gyrus	brain
40	chr7:116558400-116564600	Weak transcription	NH-A	brain
41	chr7:116558400-116564800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr7:116558400-116568400	Weak transcription	HepG2	liver
43	chr7:116558400-116570600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr7:116558400-116570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:116558400-116570600	Weak transcription	Brain Anterior Caudate	brain
46	chr7:116558400-116570800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr7:116558600-116564000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:116558600-116570400	Weak transcription	Fetal Lung	lung
49	chr7:116558600-116570600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr7:116558800-116562600	Weak transcription	NHDF-Ad	bronchial

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