Variant report

Variant	rs3739544
Chromosome Location	chr9:26962170-26962171
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10511796	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10511798	0.97[EUR][1000 genomes]
rs10757636	0.81[ASN][1000 genomes]
rs10812480	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs10812485	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10812490	0.89[AMR][1000 genomes]
rs10812491	0.89[AMR][1000 genomes]
rs10812494	0.95[JPT][hapmap];0.89[AMR][1000 genomes]
rs10812495	0.85[AMR][1000 genomes]
rs10812502	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10812503	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs10812504	0.83[ASN][1000 genomes]
rs10812505	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10812506	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10812507	0.81[JPT][hapmap]
rs10812509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10812510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10812513	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10812514	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10812517	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10812518	0.80[JPT][hapmap]
rs10812522	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10812524	0.88[EUR][1000 genomes]
rs10967560	0.85[CHB][hapmap]
rs10967566	0.80[JPT][hapmap]
rs10967581	0.84[CHB][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs10967586	0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10967597	0.90[JPT][hapmap];0.89[AMR][1000 genomes]
rs10967599	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10967602	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967609	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967611	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10967612	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10967614	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10967621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967622	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967623	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967629	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10967630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967632	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10967633	1.00[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]
rs10967635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10967636	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10967645	0.81[AFR][1000 genomes]
rs10967646	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10967649	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10967650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10967651	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10967652	0.81[JPT][hapmap]
rs10967661	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967662	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967666	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967668	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967669	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967672	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967673	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10967678	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967679	0.81[JPT][hapmap]
rs10967681	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes]
rs10967682	0.89[EUR][1000 genomes]
rs10967688	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs10967694	0.91[EUR][1000 genomes]
rs10967695	0.91[EUR][1000 genomes]
rs10967699	0.88[EUR][1000 genomes]
rs10967701	0.88[EUR][1000 genomes]
rs10967717	1.00[CEU][hapmap]
rs10967719	1.00[CEU][hapmap]
rs11534184	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11534185	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11555693	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11562224	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12235490	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12236404	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12236850	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12237867	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12684983	0.88[EUR][1000 genomes]
rs1336337	0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1541144	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs17760820	0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs17833941	1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs1970187	0.89[AFR][1000 genomes]
rs2184438	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2184439	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3737226	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3739547	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3739548	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3739550	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3758218	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs4621911	0.81[JPT][hapmap]
rs55827505	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55860736	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55870543	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56307252	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56903929	0.88[EUR][1000 genomes]
rs57450012	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57692080	0.88[EUR][1000 genomes]
rs60281060	0.91[EUR][1000 genomes]
rs60841248	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475954	0.81[JPT][hapmap]
rs7018585	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs7018943	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs7019034	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7019075	0.83[AMR][1000 genomes]
rs7020010	0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7024327	0.91[EUR][1000 genomes]
rs7031903	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7031984	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7034478	0.83[ASN][1000 genomes]
rs7034888	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7034899	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7035447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038218	0.84[JPT][hapmap]
rs7045339	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72703105	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72719536	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72719538	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7849248	0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7857447	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7857466	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7857669	0.80[JPT][hapmap]
rs7857990	0.85[AMR][1000 genomes]
rs7865952	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7869798	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7870787	0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7871668	0.81[JPT][hapmap]
rs7872496	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7872666	0.81[AMR][1000 genomes]
rs7873073	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7874940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875068	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7875171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9644870	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26957000-26973800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:26957000-26980800	Weak transcription	Lung	lung
3	chr9:26957000-26983200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:26957000-26984400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr9:26957000-27024000	Weak transcription	Esophagus	oesophagus
6	chr9:26957200-26962200	Weak transcription	Thymus	Thymus
7	chr9:26957200-26976000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:26957200-26980800	Weak transcription	Fetal Intestine Large	intestine
9	chr9:26957200-26980800	Weak transcription	Fetal Stomach	stomach
10	chr9:26957200-26982600	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:26957200-26982600	Weak transcription	Left Ventricle	heart
12	chr9:26957200-26983200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr9:26957200-26983200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:26957200-26984400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:26957200-26984400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr9:26957200-26984600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr9:26957200-26984800	Weak transcription	Primary B cells from cord blood	blood
18	chr9:26957200-26984800	Weak transcription	Fetal Thymus	thymus
19	chr9:26957200-27026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:26957200-27040000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr9:26957400-26962200	Weak transcription	Fetal Lung	lung
22	chr9:26957400-26963800	Weak transcription	NHLF	lung
23	chr9:26957400-26964800	Weak transcription	Primary T cells from cord blood	blood
24	chr9:26957400-26974800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:26957400-26978200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr9:26957400-26980800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr9:26957400-26982800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:26957400-26983200	Weak transcription	Brain Anterior Caudate	brain
29	chr9:26957400-26983400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr9:26957400-26984600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr9:26957600-26965800	Weak transcription	Fetal Brain Female	brain
32	chr9:26957600-26975200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:26957600-26979400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:26957600-26982800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:26957600-26983200	Weak transcription	Fetal Kidney	kidney
36	chr9:26957600-26983400	Weak transcription	Brain Angular Gyrus	brain
37	chr9:26957600-26984800	Weak transcription	Brain Hippocampus Middle	brain
38	chr9:26957800-26963800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:26957800-26965000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr9:26957800-26974600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:26957800-26975600	Weak transcription	Fetal Intestine Small	intestine
42	chr9:26957800-26976600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:26957800-26984600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr9:26958400-26965000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr9:26958600-26962400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr9:26958600-26965200	Weak transcription	Dnd41	blood
47	chr9:26958600-26967600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:26958600-26981000	Weak transcription	Ovary	ovary
49	chr9:26960000-26965000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr9:26960000-26971600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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