Variant report

Variant	rs2291055
Chromosome Location	chr9:5988333-5988334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10117416	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10121480	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10733517	1.00[CEU][hapmap]
rs10733520	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10733521	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733522	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733523	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739079	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10739082	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10758731	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10758732	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10758734	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes]
rs10815330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10815335	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12335590	0.88[YRI][hapmap]
rs12338275	0.84[YRI][hapmap]
rs1331378	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1331379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1418740	1.00[CEU][hapmap]
rs1478935	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1478936	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1478937	0.81[ASN][1000 genomes]
rs1478938	0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs16923578	1.00[CEU][hapmap]
rs186913	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1888703	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs1888704	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2150703	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2169906	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2244053	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs2244058	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs2381341	0.81[ASN][1000 genomes]
rs2381360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2890690	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs343469	1.00[CEU][hapmap]
rs343471	1.00[CEU][hapmap]
rs343480	1.00[CEU][hapmap]
rs343482	1.00[CEU][hapmap]
rs343500	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs3739649	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3933800	0.80[ASN][1000 genomes]
rs4075225	1.00[CEU][hapmap]
rs4265236	1.00[CEU][hapmap]
rs4389996	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4395943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4421399	0.83[ASN][1000 genomes]
rs4740833	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4740834	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4742131	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs4742141	0.90[ASN][1000 genomes]
rs4742142	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742143	0.96[ASN][1000 genomes]
rs6477017	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs6477021	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6477022	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6477023	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6477024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477025	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6477026	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7019606	1.00[CEU][hapmap]
rs7021498	1.00[CEU][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7024130	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7026453	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7026454	0.84[CHB][hapmap];0.83[JPT][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7029833	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7030731	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7032130	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7034210	1.00[CEU][hapmap]
rs7042947	1.00[CEU][hapmap]
rs7044750	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7851268	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7851749	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7866793	1.00[CEU][hapmap]
rs7868062	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7869571	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7875450	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5940000-6006800	Weak transcription	Gastric	stomach
2	chr9:5948000-6006000	Weak transcription	Right Ventricle	heart
3	chr9:5950600-6006000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:5955000-5993600	Weak transcription	Lung	lung
5	chr9:5957400-6004400	Weak transcription	Brain Germinal Matrix	brain
6	chr9:5957600-5991800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:5967000-5996600	Weak transcription	Brain Angular Gyrus	brain
8	chr9:5967200-6006000	Weak transcription	Colonic Mucosa	Colon
9	chr9:5968400-6005600	Weak transcription	Fetal Kidney	kidney
10	chr9:5969200-5996800	Weak transcription	HMEC	breast
11	chr9:5969400-5999600	Weak transcription	HSMMtube	muscle
12	chr9:5972200-6005800	Weak transcription	NH-A	brain
13	chr9:5973600-5990600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:5974000-5989000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:5974000-5990800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:5974000-5991400	Weak transcription	Esophagus	oesophagus
17	chr9:5974000-6006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:5974400-5999600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr9:5974800-5990600	Weak transcription	HepG2	liver
20	chr9:5974800-6001000	Weak transcription	Fetal Brain Female	brain
21	chr9:5975200-6005800	Weak transcription	Fetal Stomach	stomach
22	chr9:5977200-5989400	Weak transcription	HUVEC	blood vessel
23	chr9:5977200-5997000	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:5977400-5988400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:5977400-5993400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:5977400-5994400	Weak transcription	K562	blood
27	chr9:5977400-5996200	Weak transcription	Psoas Muscle	Psoas
28	chr9:5977400-5996600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:5977400-5996800	Weak transcription	Stomach Mucosa	stomach
30	chr9:5977400-6000800	Weak transcription	Small Intestine	intestine
31	chr9:5977400-6004800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr9:5977400-6005600	Weak transcription	NHLF	lung
33	chr9:5977400-6005800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr9:5977400-6006800	Weak transcription	Pancreas	Pancrea
35	chr9:5977400-6007000	Weak transcription	Spleen	Spleen
36	chr9:5978600-5988800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr9:5978800-5994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr9:5980000-5988600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr9:5980400-5988600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:5982600-5991200	Weak transcription	Aorta	Aorta
41	chr9:5982600-5995600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:5982800-5993600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr9:5982800-5999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr9:5982800-6005200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr9:5983200-5993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:5983200-5993600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr9:5983200-5996800	Weak transcription	NHEK	skin
48	chr9:5983200-5999400	Weak transcription	Brain Substantia Nigra	brain
49	chr9:5983200-6004200	Weak transcription	Osteobl	bone
50	chr9:5983400-5988400	Weak transcription	Ovary	ovary

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