Variant report

Variant	rs676686
Chromosome Location	chr1:97698637-97698638
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10875055	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs11165810	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs17116488	0.89[JPT][hapmap]
rs17116518	0.83[JPT][hapmap]
rs17116594	0.90[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1970143	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4128473	0.89[JPT][hapmap]
rs4412640	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656660	0.89[JPT][hapmap]
rs7529372	0.89[JPT][hapmap]
rs885621	0.92[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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97690400-97698800	Weak transcription	Brain Substantia Nigra	brain
2	chr1:97691400-97701000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:97691400-97702600	Weak transcription	Fetal Intestine Small	intestine
4	chr1:97692800-97703400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:97693000-97701800	Weak transcription	Fetal Lung	lung
6	chr1:97693200-97700800	Weak transcription	Pancreas	Pancrea
7	chr1:97694000-97699600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:97694400-97698800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:97694800-97698800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:97694800-97698800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:97694800-97701000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:97694800-97712800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:97695400-97698800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:97695800-97700000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:97696000-97698800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:97696000-97701000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:97697000-97700000	Strong transcription	Liver	Liver
18	chr1:97697000-97711000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:97697200-97698800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:97697200-97698800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:97697200-97710800	Weak transcription	Osteobl	bone
22	chr1:97697400-97699000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:97697400-97700000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:97697400-97700600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:97697400-97700600	Strong transcription	Dnd41	blood
26	chr1:97697400-97711400	Weak transcription	Brain Anterior Caudate	brain
27	chr1:97697800-97700600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:97697800-97700600	Weak transcription	Thymus	Thymus
29	chr1:97697800-97704000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:97698000-97699400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:97698000-97700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:97698000-97700200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:97698000-97708000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:97698200-97700600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:97698200-97701000	Weak transcription	Right Ventricle	heart
36	chr1:97698400-97699600	Strong transcription	Primary hematopoietic stem cells	blood
37	chr1:97698400-97700200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:97698400-97700600	Strong transcription	HSMM	muscle
39	chr1:97698400-97700800	Strong transcription	Primary B cells from cord blood	blood
40	chr1:97698600-97698800	Strong transcription	Gastric	stomach
41	chr1:97698600-97699000	ZNF genes & repeats	Lung	lung
42	chr1:97698600-97699000	Genic enhancers	Spleen	Spleen
43	chr1:97698600-97699200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:97698600-97699200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:97698600-97699200	Strong transcription	Fetal Brain Female	brain
46	chr1:97698600-97699200	Strong transcription	Rectal Smooth Muscle	rectum
47	chr1:97698600-97699400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:97698600-97699400	Strong transcription	Esophagus	oesophagus
49	chr1:97698600-97699400	Strong transcription	Fetal Intestine Large	intestine
50	chr1:97698600-97699400	Strong transcription	Ovary	ovary

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