Variant report

Variant	rs927639
Chromosome Location	chr10:98359014-98359015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:98352916..98354492-chr10:98357583..98359914,2	K562	blood:
2	chr10:98357043..98359893-chr10:98362984..98364964,2	K562	blood:
3	chr10:98344272..98346550-chr10:98357968..98360744,2	K562	blood:
4	chr10:98345226..98348138-chr10:98356435..98359434,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077147	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10128106	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1018604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1018605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1051450	0.83[ASN][1000 genomes]
rs1063605	0.83[ASN][1000 genomes]
rs10736114	0.87[CEU][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10882811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10882813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10882817	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10882826	0.87[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882827	0.91[ASN][1000 genomes]
rs10882828	0.90[CEU][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11188822	0.84[JPT][hapmap]
rs11188827	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11188831	0.81[ASN][1000 genomes]
rs11188832	0.81[ASN][1000 genomes]
rs11188833	0.81[ASN][1000 genomes]
rs11188840	0.86[ASN][1000 genomes]
rs11188842	0.83[ASN][1000 genomes]
rs11188844	0.83[ASN][1000 genomes]
rs11188847	0.88[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs11188848	0.91[ASN][1000 genomes]
rs11188853	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11188854	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11188856	0.91[CEU][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11188857	0.83[ASN][1000 genomes]
rs11188858	0.81[ASN][1000 genomes]
rs12219275	0.81[ASN][1000 genomes]
rs12220047	0.81[ASN][1000 genomes]
rs12776810	0.83[ASN][1000 genomes]
rs1324256	0.81[ASN][1000 genomes]
rs1324258	1.00[CEU][hapmap]
rs1324259	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1324261	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1408367	0.81[ASN][1000 genomes]
rs1983831	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2025451	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2031326	0.81[ASN][1000 genomes]
rs2031329	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2861555	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36098523	0.91[ASN][1000 genomes]
rs3748234	0.92[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3748235	0.89[ASW][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3748236	0.89[ASN][1000 genomes]
rs3748237	0.83[ASN][1000 genomes]
rs3789957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3818389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4146727	0.88[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs4917742	0.87[CEU][hapmap];0.92[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4919029	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4919032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4919037	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4919040	0.80[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58305369	0.91[ASN][1000 genomes]
rs61858194	0.89[ASN][1000 genomes]
rs61859300	0.83[ASN][1000 genomes]
rs7070686	0.83[ASN][1000 genomes]
rs7071044	0.83[ASN][1000 genomes]
rs7071881	0.83[ASN][1000 genomes]
rs7073017	0.91[ASN][1000 genomes]
rs7073682	0.91[ASN][1000 genomes]
rs7074516	0.83[ASN][1000 genomes]
rs7082873	0.81[ASN][1000 genomes]
rs7085389	0.83[ASN][1000 genomes]
rs7086213	0.83[ASN][1000 genomes]
rs7091606	0.91[ASN][1000 genomes]
rs7097291	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7101320	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727329	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7448	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7478356	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7914154	0.92[JPT][hapmap];0.91[MEX][hapmap]
rs7919739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8578	0.83[ASN][1000 genomes]
rs912480	0.87[CEU][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9633703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv895909	chr10:98354924-98382165	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs927639	NPM1P26	cis	Esophagus Muscularis	GTEx
rs927639	NPM1P26	cis	Stomach	GTEx
rs927639	NPM1P26	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98347800-98365800	Weak transcription	Ovary	ovary
2	chr10:98348000-98373600	Weak transcription	Left Ventricle	heart
3	chr10:98349800-98366400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr10:98349800-98367800	Weak transcription	Small Intestine	intestine
5	chr10:98350800-98395600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr10:98351600-98363400	Weak transcription	Brain Hippocampus Middle	brain
7	chr10:98352400-98378600	Strong transcription	Liver	Liver
8	chr10:98352400-98399400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr10:98352600-98369400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:98352600-98403000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr10:98353000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:98353000-98403000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr10:98353600-98362800	Strong transcription	Primary hematopoietic stem cells	blood
14	chr10:98354200-98360800	Enhancers	Fetal Intestine Large	intestine
15	chr10:98354600-98360800	Strong transcription	Primary B cells from cord blood	blood
16	chr10:98354600-98388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:98354800-98370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr10:98355200-98360800	Enhancers	Stomach Mucosa	stomach
19	chr10:98356200-98362400	Weak transcription	Lung	lung
20	chr10:98356200-98367200	Weak transcription	Colonic Mucosa	Colon
21	chr10:98357400-98364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:98357600-98369200	Weak transcription	HepG2	liver
23	chr10:98357800-98382000	Strong transcription	GM12878-XiMat	blood
24	chr10:98358000-98360400	Enhancers	Fetal Intestine Small	intestine
25	chr10:98358200-98360800	Enhancers	HSMMtube	muscle
26	chr10:98358400-98360600	Enhancers	Duodenum Mucosa	Duodenum
27	chr10:98358400-98360600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr10:98358400-98363200	Strong transcription	Spleen	Spleen
29	chr10:98358600-98359200	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr10:98358600-98359400	Enhancers	Right Ventricle	heart
31	chr10:98358600-98360400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr10:98358600-98370400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr10:98358800-98359400	Strong transcription	Pancreas	Pancrea
34	chr10:98358800-98369600	Weak transcription	Gastric	stomach
35	chr10:98359000-98362000	Weak transcription	Placenta	Placenta

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