Variant report

Variant	rs1983831
Chromosome Location	chr10:98371748-98371749
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:98366804..98369956-chr10:98370785..98374405,6	K562	blood:
2	chr10:98346216..98348806-chr10:98369688..98372310,2	K562	blood:
3	chr10:98367008..98370019-chr10:98371148..98375452,4	K562	blood:
4	chr10:98346216..98350490-chr10:98369688..98376085,7	K562	blood:

Variant related genes	Relation type
ENSG00000077147	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1018604	0.92[JPT][hapmap]
rs1018605	0.92[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs10736114	0.81[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882811	0.92[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs10882813	0.92[JPT][hapmap]
rs10882826	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882827	0.86[ASN][1000 genomes]
rs10882828	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188822	0.84[JPT][hapmap]
rs11188847	0.87[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs11188848	0.80[ASN][1000 genomes]
rs11188853	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11188854	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188856	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188857	0.94[ASN][1000 genomes]
rs1324261	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36098523	0.80[ASN][1000 genomes]
rs3748234	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3748235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3748236	0.82[ASN][1000 genomes]
rs3789957	0.92[JPT][hapmap]
rs3818389	0.92[JPT][hapmap]
rs4146727	0.87[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4917742	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4919029	0.92[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs4919032	0.92[JPT][hapmap]
rs4919040	0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58305369	0.80[ASN][1000 genomes]
rs7073017	0.80[ASN][1000 genomes]
rs7073682	0.80[ASN][1000 genomes]
rs7091606	0.80[ASN][1000 genomes]
rs7101320	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs727329	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7448	0.92[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs7478356	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914154	0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs7919739	0.92[JPT][hapmap]
rs912480	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs927639	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]
rs9633703	0.92[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]

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	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
3	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1983831	NPM1P26	cis	Stomach	GTEx
rs1983831	NPM1P26	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98348000-98373600	Weak transcription	Left Ventricle	heart
2	chr10:98350800-98395600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr10:98352400-98378600	Strong transcription	Liver	Liver
4	chr10:98352400-98399400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr10:98352600-98403000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr10:98353000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:98353000-98403000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr10:98354600-98388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:98357800-98382000	Strong transcription	GM12878-XiMat	blood
10	chr10:98359400-98373400	Weak transcription	Right Ventricle	heart
11	chr10:98360400-98392800	Weak transcription	Thymus	Thymus
12	chr10:98362200-98389200	Strong transcription	Primary B cells from cord blood	blood
13	chr10:98362600-98373600	Weak transcription	Lung	lung
14	chr10:98363800-98392600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr10:98365600-98374200	Enhancers	Fetal Intestine Large	intestine
16	chr10:98365600-98374400	Enhancers	Fetal Intestine Small	intestine
17	chr10:98366000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:98366400-98373400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:98366600-98392600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr10:98367200-98372800	Strong transcription	Pancreas	Pancrea
21	chr10:98367200-98375000	Enhancers	Stomach Mucosa	stomach
22	chr10:98367200-98376200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:98367400-98375000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr10:98367400-98376200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr10:98367400-98418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr10:98367600-98372000	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr10:98367800-98371800	Enhancers	Colonic Mucosa	Colon
28	chr10:98368400-98373600	Weak transcription	HSMM	muscle
29	chr10:98368600-98371800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:98368800-98377800	Weak transcription	Brain Anterior Caudate	brain
31	chr10:98369000-98373400	Weak transcription	HSMMtube	muscle
32	chr10:98369200-98372600	Enhancers	HepG2	liver
33	chr10:98370000-98373600	Weak transcription	Gastric	stomach
34	chr10:98370600-98372200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr10:98370600-98375800	Weak transcription	Ovary	ovary
36	chr10:98370800-98373600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr10:98370800-98378600	Weak transcription	Brain Substantia Nigra	brain
38	chr10:98371000-98371800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr10:98371000-98378800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr10:98371000-98382600	Strong transcription	Spleen	Spleen
41	chr10:98371000-98388600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr10:98371000-98389000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr10:98371200-98372400	Enhancers	Duodenum Mucosa	Duodenum
44	chr10:98371200-98373200	Weak transcription	Placenta	Placenta
45	chr10:98371200-98373200	Weak transcription	K562	blood
46	chr10:98371200-98373600	Weak transcription	Small Intestine	intestine
47	chr10:98371200-98375000	Weak transcription	Primary T cells fromperipheralblood	blood

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