Variant report

Variant	rs2152358
Chromosome Location	chr1:93634009-93634010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93632484..93634850-chr1:93639187..93641341,2	K562	blood:
2	chr1:93631724..93634968-chr1:93643710..93645431,3	K562	blood:

Extended variants
information (count: 127 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1010476	0.82[CHB][hapmap]
rs1057257	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782955	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10782957	0.84[EUR][1000 genomes]
rs10782959	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs10874759	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874762	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10874764	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1088318	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11164870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164871	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164876	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11164879	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11164880	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164881	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11164908	0.87[CHB][hapmap]
rs12030549	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12030843	0.87[CHB][hapmap]
rs12033147	0.85[CHB][hapmap]
rs12038699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12044557	0.86[CHB][hapmap]
rs12044657	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12044883	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12118230	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12118262	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12124011	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12124771	0.83[EUR][1000 genomes]
rs12128131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12130734	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12133576	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12139009	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12139633	0.86[EUR][1000 genomes]
rs12385720	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12563120	0.86[CHB][hapmap]
rs1335679	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474927	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1535701	0.83[EUR][1000 genomes]
rs1537758	0.87[ASN][1000 genomes]
rs1559828	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1572343	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1856027	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1932314	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1967721	0.89[ASN][1000 genomes]
rs2031225	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2031226	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2208044	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2255722	0.82[CHB][hapmap]
rs2281524	0.82[CHB][hapmap]
rs2281525	0.83[CHB][hapmap]
rs2295423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2295424	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2296558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2297707	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2391254	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2484486	0.81[CHB][hapmap]
rs2765545	0.91[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2783489	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs2783490	0.82[CHB][hapmap]
rs2783495	0.82[CHB][hapmap]
rs2783499	0.86[CHB][hapmap]
rs2783500	0.86[CHB][hapmap]
rs2783501	0.87[CHB][hapmap]
rs35940311	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3754184	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3754186	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3767964	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3904666	0.82[CHB][hapmap]
rs4000699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs4240966	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4484937	0.86[CHB][hapmap]
rs4847235	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847240	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4847398	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4847399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4847401	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847402	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4847408	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs531358	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs531514	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs535760	0.83[AMR][1000 genomes]
rs547866	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs555161	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs565919	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs569414	0.91[CEU][hapmap]
rs602204	0.83[AMR][1000 genomes]
rs612037	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61799471	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs622608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs624131	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs627779	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs637646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6541349	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6541401	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs6541404	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs6682670	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6688230	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6703310	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs682514	0.82[AMR][1000 genomes]
rs687394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs693737	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs7418101	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7512911	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7513705	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7517363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7525248	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7532195	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7532549	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7535628	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7539307	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7541687	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7553465	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7553916	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs797661	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs797666	0.83[AMR][1000 genomes]
rs797668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs797671	0.82[AMR][1000 genomes]
rs797672	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs797675	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs797676	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs797680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs797681	0.86[AMR][1000 genomes]
rs942196	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9432459	0.86[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2152358	DR1	cis	multi-tissue	Pritchard
rs2152358	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs2152358	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs2152358	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2152358	RP4-717I23.3	cis	Artery Aorta	GTEx
rs2152358	RP4-717I23.3	cis	lung	GTEx
rs2152358	RP4-717I23.3	cis	Whole Blood	GTEx
rs2152358	RP4-717I23.3	cis	Artery Tibial	GTEx
rs2152358	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs2152358	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs2152358	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs2152358	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs2152358	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs2152358	RP4-717I23.3	cis	Thyroid	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:93582400-93642800	Weak transcription	Gastric	stomach
3	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
4	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
5	chr1:93595800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:93600400-93635400	Weak transcription	Spleen	Spleen
7	chr1:93601000-93643600	Weak transcription	HSMMtube	muscle
8	chr1:93601400-93635400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:93606000-93644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:93606800-93635400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:93611800-93644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:93614200-93634800	Weak transcription	A549	lung
13	chr1:93615600-93643200	Weak transcription	Fetal Kidney	kidney
14	chr1:93620800-93635600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:93621400-93635400	Weak transcription	Thymus	Thymus
16	chr1:93621400-93635600	Weak transcription	Lung	lung
17	chr1:93621400-93636800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:93621400-93637800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:93621400-93640000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:93621400-93643000	Weak transcription	HMEC	breast
21	chr1:93621400-93643800	Weak transcription	Colonic Mucosa	Colon
22	chr1:93621600-93641400	Weak transcription	NHEK	skin
23	chr1:93622200-93637200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:93622400-93636400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:93624000-93637200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:93624000-93643400	Weak transcription	NH-A	brain
27	chr1:93624000-93643600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:93624200-93636400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:93624400-93643600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:93624800-93636400	Weak transcription	Primary T cells from cord blood	blood
31	chr1:93624800-93641600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:93624800-93643600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:93624800-93643600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:93625000-93636600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:93625000-93640000	Weak transcription	K562	blood
36	chr1:93625000-93641200	Weak transcription	HSMM	muscle
37	chr1:93625200-93635400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:93625200-93637200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:93625400-93636600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:93625600-93634600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:93625600-93634800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:93625600-93637600	Weak transcription	NHLF	lung
43	chr1:93625800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:93625800-93635800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:93625800-93637000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:93625800-93637400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:93625800-93640200	Weak transcription	HUVEC	blood vessel
48	chr1:93625800-93641600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:93625800-93643400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:93626000-93635200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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