Variant report

Variant	rs1097929
Chromosome Location	chr2:234415666-234415667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10169180	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10177112	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10178062	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10178357	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10183033	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10185923	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10198879	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10207915	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10208361	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1037451	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10803653	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10929195	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10929200	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10929208	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1097930	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1097931	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11690686	0.95[EUR][1000 genomes]
rs1220430	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12467878	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12473743	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12473824	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12615446	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12692193	0.98[EUR][1000 genomes]
rs12692195	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13002253	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13018364	0.96[EUR][1000 genomes]
rs1377459	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1377461	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1453321	0.97[EUR][1000 genomes]
rs1470864	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1470865	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1542325	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1542326	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1545524	0.80[EUR][1000 genomes]
rs1545525	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1597940	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1901812	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2034675	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2124045	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2167884	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2167885	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2602387	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2602389	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2603545	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2603546	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2603547	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2924809	0.93[EUR][1000 genomes]
rs2924811	0.91[EUR][1000 genomes]
rs2924813	0.89[EUR][1000 genomes]
rs2971861	0.93[EUR][1000 genomes]
rs2971862	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2971863	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2971864	0.96[EUR][1000 genomes]
rs2971865	0.93[EUR][1000 genomes]
rs2971866	0.93[EUR][1000 genomes]
rs2971867	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2971869	0.87[EUR][1000 genomes]
rs2971870	0.91[EUR][1000 genomes]
rs2971871	0.91[EUR][1000 genomes]
rs2971872	0.91[EUR][1000 genomes]
rs4047187	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4047188	0.96[EUR][1000 genomes]
rs4047198	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4047199	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4233627	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4663684	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4663698	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55679565	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59160392	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6710645	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6710772	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6716988	0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6720619	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6726184	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6753062	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6756068	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7557849	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567713	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7571288	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7572310	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7575694	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7578898	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7599285	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7603410	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7604337	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7724	0.93[EUR][1000 genomes]
rs838543	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs838544	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs838545	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs838548	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs838549	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs838550	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs838551	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs838552	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs838555	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs838557	0.98[EUR][1000 genomes]
rs838558	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs838559	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs838561	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs838562	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs860794	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs896833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv3214	chr2:234384436-234416949	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr2:234390800-234441000	Weak transcription	Fetal Brain Male	brain
3	chr2:234395600-234431800	Weak transcription	Colonic Mucosa	Colon
4	chr2:234398000-234452800	Weak transcription	HUVEC	blood vessel
5	chr2:234398400-234442400	Weak transcription	Hela-S3	cervix
6	chr2:234398600-234431800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:234400400-234430000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:234401200-234430800	Weak transcription	NHLF	lung
9	chr2:234402200-234472400	Weak transcription	Psoas Muscle	Psoas
10	chr2:234402600-234429800	Weak transcription	Right Ventricle	heart
11	chr2:234402600-234430600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:234402600-234436800	Weak transcription	Gastric	stomach
13	chr2:234402600-234454000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:234404400-234455000	Weak transcription	Fetal Thymus	thymus
15	chr2:234405000-234431200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:234407600-234419600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:234407800-234431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:234407800-234436800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:234410000-234416000	Strong transcription	Fetal Kidney	kidney
20	chr2:234410400-234428000	Weak transcription	NHDF-Ad	bronchial
21	chr2:234410600-234427200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:234410600-234428200	Weak transcription	Osteobl	bone
23	chr2:234410800-234429800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:234411200-234416400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr2:234411400-234419600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:234411400-234430000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:234411400-234430000	Weak transcription	Aorta	Aorta
28	chr2:234411400-234432400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:234411600-234418600	Weak transcription	Ovary	ovary
30	chr2:234411600-234421800	Weak transcription	Left Ventricle	heart
31	chr2:234411600-234422600	Weak transcription	Brain Angular Gyrus	brain
32	chr2:234411600-234427400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr2:234411600-234427400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:234411600-234427600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:234411600-234429800	Weak transcription	Pancreas	Pancrea
36	chr2:234411600-234431800	Weak transcription	Lung	lung
37	chr2:234411600-234465600	Weak transcription	Thymus	Thymus
38	chr2:234412000-234416600	Strong transcription	HSMM	muscle
39	chr2:234412200-234425000	Weak transcription	Fetal Intestine Small	intestine
40	chr2:234412400-234416400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:234412400-234437600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:234412600-234417400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:234412600-234420000	Strong transcription	Liver	Liver
44	chr2:234412600-234421800	Weak transcription	HSMMtube	muscle
45	chr2:234412600-234422600	Weak transcription	HMEC	breast
46	chr2:234412600-234437400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:234412800-234418200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr2:234412800-234427400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:234413000-234415800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:234413000-234422000	Weak transcription	Colon Smooth Muscle	Colon

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