Variant report

Variant	rs6477160
Chromosome Location	chr9:7116679-7116680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10122120	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs10491781	0.82[ASN][1000 genomes]
rs10491782	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1073496	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10758826	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10758827	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10758828	0.81[CEU][hapmap];0.92[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10758829	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10758830	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10758831	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10758832	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10815518	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10815519	0.82[CEU][hapmap]
rs10815520	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10976045	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10976047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10976052	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12686272	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1323404	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323405	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323406	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323407	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025324	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3763651	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs3802400	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802403	1.00[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4740871	0.87[YRI][hapmap]
rs6477158	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6477159	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6477161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021692	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7023759	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7023789	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028048	0.84[ASN][1000 genomes]
rs7037866	0.82[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7048573	0.94[CHB][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7858101	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7860305	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7862227	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862711	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7867958	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7869012	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7869317	0.86[CHB][hapmap];0.94[ASN][1000 genomes]
rs7872366	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872504	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872625	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299041	0.93[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers 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	4 gene(s)	inside rSNPs	diseases
4	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv869932	chr9:7068359-7133384	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv892189	chr9:7091968-7150997	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv892190	chr9:7094860-7186074	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7088800-7128000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:7098600-7118000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:7100800-7120200	Strong transcription	Primary B cells from cord blood	blood
4	chr9:7103000-7148600	Strong transcription	Primary B cells from peripheral blood	blood
5	chr9:7103600-7118600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:7103800-7128800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:7104000-7117800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:7104000-7121200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr9:7104200-7117800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:7104200-7118000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:7104200-7118000	Weak transcription	HMEC	breast
12	chr9:7104200-7123600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:7104200-7128200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:7104200-7148200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr9:7104400-7121200	Weak transcription	Esophagus	oesophagus
16	chr9:7104400-7121200	Weak transcription	Pancreas	Pancrea
17	chr9:7104400-7123600	Weak transcription	Gastric	stomach
18	chr9:7104400-7128000	Weak transcription	Aorta	Aorta
19	chr9:7104400-7128000	Weak transcription	Lung	lung
20	chr9:7104400-7135400	Weak transcription	Fetal Muscle Leg	muscle
21	chr9:7104400-7137600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr9:7104400-7144600	Weak transcription	Brain Anterior Caudate	brain
23	chr9:7104600-7148000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:7104800-7117800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:7104800-7120000	Weak transcription	Small Intestine	intestine
26	chr9:7104800-7123400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr9:7104800-7138200	Weak transcription	HSMM	muscle
28	chr9:7104800-7142800	Weak transcription	Osteobl	bone
29	chr9:7104800-7153200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:7105000-7118600	Weak transcription	Placenta	Placenta
31	chr9:7105000-7121400	Weak transcription	Spleen	Spleen
32	chr9:7105000-7133600	Weak transcription	Fetal Stomach	stomach
33	chr9:7105000-7146600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:7105200-7117800	Weak transcription	NHDF-Ad	bronchial
35	chr9:7105200-7123800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:7105200-7130200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr9:7105400-7117800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:7105400-7118800	Weak transcription	Psoas Muscle	Psoas
39	chr9:7105400-7120200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr9:7105400-7120600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr9:7105400-7121600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr9:7105400-7128200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr9:7105600-7121200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr9:7105600-7123400	Weak transcription	HepG2	liver
45	chr9:7105600-7123600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr9:7105600-7128200	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:7105600-7133200	Weak transcription	Ovary	ovary
48	chr9:7105600-7136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:7105800-7118000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:7105800-7121200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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