Variant report

Variant	rs17116594
Chromosome Location	chr1:97701403-97701404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11165810	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12564297	0.88[GIH][hapmap];0.88[MEX][hapmap]
rs12735722	0.94[GIH][hapmap];0.88[MEX][hapmap]
rs17116488	0.94[JPT][hapmap];1.00[MEX][hapmap]
rs17116518	0.88[JPT][hapmap]
rs1970143	0.96[ASN][1000 genomes]
rs4128473	0.81[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap]
rs4412640	0.89[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4950025	0.94[GIH][hapmap];0.88[MEX][hapmap]
rs58951949	0.81[AMR][1000 genomes]
rs6656660	0.81[CHD][hapmap];0.94[JPT][hapmap]
rs676686	0.90[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs7528631	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7529372	0.81[CHD][hapmap];0.94[JPT][hapmap]
rs885621	0.97[AMR][1000 genomes];0.95[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	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97691400-97702600	Weak transcription	Fetal Intestine Small	intestine
2	chr1:97692800-97703400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:97693000-97701800	Weak transcription	Fetal Lung	lung
4	chr1:97694800-97712800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:97697000-97711000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:97697200-97710800	Weak transcription	Osteobl	bone
7	chr1:97697400-97711400	Weak transcription	Brain Anterior Caudate	brain
8	chr1:97697800-97704000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:97698000-97708000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:97699200-97702000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:97699200-97702000	Weak transcription	Aorta	Aorta
12	chr1:97699200-97704000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:97699200-97710800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:97699400-97701800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:97699400-97702000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:97699400-97706800	Weak transcription	Ovary	ovary
17	chr1:97699400-97709400	Weak transcription	Brain Substantia Nigra	brain
18	chr1:97699400-97710800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:97699400-97711000	Weak transcription	Fetal Intestine Large	intestine
20	chr1:97699400-97723600	Weak transcription	Lung	lung
21	chr1:97699600-97701600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:97699600-97702600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:97699600-97710000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:97699600-97711000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:97699600-97711200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:97699600-97711200	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:97699600-97729000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:97699800-97702000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:97699800-97710800	Weak transcription	Adipose Nuclei	Adipose
30	chr1:97700000-97702200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:97700000-97705600	Weak transcription	Liver	Liver
32	chr1:97700000-97710600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:97700000-97711400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:97700000-97717800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:97700200-97701800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:97700200-97702800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:97700400-97702200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:97700600-97702200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:97700600-97702200	Weak transcription	HSMM	muscle
40	chr1:97700600-97703400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:97700600-97706600	Weak transcription	Primary T cells from cord blood	blood
42	chr1:97700600-97710800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:97700600-97711400	Weak transcription	Left Ventricle	heart
44	chr1:97700600-97712200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr1:97700600-97723600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:97700600-97733000	Weak transcription	Dnd41	blood
47	chr1:97700800-97702600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:97700800-97711000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:97700800-97712400	Weak transcription	Primary B cells from cord blood	blood
50	chr1:97701000-97702800	Weak transcription	Primary monocytes fromperipheralblood	blood

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