Variant report

Variant	rs1890138
Chromosome Location	chr1:97839016-97839017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10875076	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875079	0.82[CHB][hapmap]
rs1112314	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs11165855	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11165856	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11165861	0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs11165863	0.81[CEU][hapmap];0.81[GIH][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs11165867	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11165868	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12021567	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs12022771	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs12026223	0.84[CEU][hapmap]
rs12030316	0.83[AFR][1000 genomes]
rs12032384	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12040388	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs12040699	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs12040763	0.90[CEU][hapmap];0.80[GIH][hapmap];0.89[MKK][hapmap]
rs12043021	0.90[CEU][hapmap]
rs12043040	0.90[CEU][hapmap]
rs12043125	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs12045127	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12046771	0.80[MKK][hapmap]
rs12047072	0.90[CEU][hapmap];0.81[GIH][hapmap]
rs12047625	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs12089260	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12096100	0.81[AFR][1000 genomes]
rs12411169	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12565467	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12566907	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12568621	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1356917	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs1415683	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1556794	0.81[ASN][1000 genomes]
rs1915313	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300257	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs4319377	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4336888	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4381229	0.81[AFR][1000 genomes]
rs4428925	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[MKK][hapmap]
rs4445510	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs4495747	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs4497250	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4503384	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs56000287	0.87[AFR][1000 genomes]
rs57676409	0.80[AFR][1000 genomes]
rs58516533	0.81[AFR][1000 genomes]
rs59111295	0.85[ASN][1000 genomes]
rs6677502	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs6678858	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6687374	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6690816	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6693628	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6701322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72728414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72728416	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72728428	0.85[AFR][1000 genomes]
rs72728429	0.85[AFR][1000 genomes]
rs72728435	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7516781	0.90[CEU][hapmap]
rs7523609	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527030	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs7535930	0.86[ASN][1000 genomes]
rs7540201	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7541618	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7543523	0.86[ASN][1000 genomes]
rs7543614	0.86[ASN][1000 genomes]
rs7544128	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7548189	0.90[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap]
rs7555984	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv546865	chr1:97838887-97874663	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97794600-97848200	Weak transcription	Left Ventricle	heart
2	chr1:97802200-97848600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:97803200-97843200	Weak transcription	Spleen	Spleen
4	chr1:97805800-97846800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:97816000-97843200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:97818000-97844200	Weak transcription	Osteobl	bone
7	chr1:97820200-97848200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:97823800-97845600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:97824000-97846800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:97824200-97843200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:97824200-97843200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:97824200-97846800	Weak transcription	Fetal Intestine Small	intestine
13	chr1:97824200-97848000	Weak transcription	Ovary	ovary
14	chr1:97824400-97855000	Weak transcription	Lung	lung
15	chr1:97827600-97847200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:97828000-97843200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:97828800-97849800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:97829200-97851000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:97829800-97845000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:97830200-97839600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:97830400-97848400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:97830600-97845000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:97830800-97843200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:97831000-97843000	Weak transcription	NH-A	brain
25	chr1:97831000-97874800	Weak transcription	HSMM	muscle
26	chr1:97832600-97843200	Weak transcription	NHDF-Ad	bronchial
27	chr1:97832800-97846200	Weak transcription	Primary B cells from cord blood	blood
28	chr1:97832800-97847800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:97832800-97861200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:97833200-97840000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:97833400-97846000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:97833800-97845200	Weak transcription	Dnd41	blood
33	chr1:97836200-97843000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:97837200-97877600	Weak transcription	Adipose Nuclei	Adipose
35	chr1:97838200-97839400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:97838600-97839200	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr1:97838600-97839400	Strong transcription	Liver	Liver
38	chr1:97839000-97839200	Enhancers	Fetal Stomach	stomach
39	chr1:97839000-97843200	Weak transcription	Primary T cells from cord blood	blood

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