Variant report

Variant	rs10800435
Chromosome Location	chr1:169323542-169323543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1018831	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10429893	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs10465575	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10465576	0.83[AMR][1000 genomes]
rs10489189	0.83[AMR][1000 genomes]
rs10732287	0.82[JPT][hapmap]
rs10753786	0.82[CEU][hapmap];0.93[YRI][hapmap]
rs10800408	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10800424	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10800425	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10800438	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10800439	0.82[CEU][hapmap]
rs10800440	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919124	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs10919132	0.82[CEU][hapmap];0.93[YRI][hapmap]
rs10919174	0.82[JPT][hapmap]
rs1124843	0.83[AMR][1000 genomes]
rs1133814	0.83[AMR][1000 genomes]
rs1200079	0.82[JPT][hapmap]
rs1200083	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap]
rs1200085	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1200164	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12029566	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12076993	0.83[AMR][1000 genomes]
rs1208135	0.82[JPT][hapmap]
rs1208370	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1208377	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs1400836	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes]
rs1400839	0.80[AMR][1000 genomes]
rs1517744	0.82[JPT][hapmap]
rs1517747	0.82[JPT][hapmap]
rs1591733	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs16861990	0.82[JPT][hapmap]
rs1856303	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs1914505	0.83[AMR][1000 genomes]
rs1983546	0.82[JPT][hapmap]
rs2003653	0.83[AMR][1000 genomes]
rs2037250	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs2066000	0.80[AMR][1000 genomes]
rs2138898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2176473	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2176474	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2300158	0.83[CEU][hapmap];0.93[YRI][hapmap]
rs3766057	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766095	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs3820059	0.83[AMR][1000 genomes]
rs3905328	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes]
rs4264046	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs4454599	0.87[AMR][1000 genomes]
rs4656183	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes]
rs4656672	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs6427185	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs6427187	0.81[AMR][1000 genomes]
rs6656822	0.82[JPT][hapmap]
rs6662237	0.80[AMR][1000 genomes]
rs6669901	0.84[AMR][1000 genomes]
rs6686204	0.84[EUR][1000 genomes]
rs7415756	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7533257	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs7544221	0.83[AMR][1000 genomes]
rs7554689	0.81[AMR][1000 genomes]
rs760603	0.83[AMR][1000 genomes]
rs925892	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs932301	0.83[AMR][1000 genomes]
rs994986	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv3404638	chr1:169322853-169325701	Weak transcription Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3371577	chr1:169323203-169325576	Weak transcription Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10800435	NME7	cis	Nerve Tibial	GTEx
rs10800435	NME7	cis	Artery Aorta	GTEx
rs10800435	NME7	cis	Esophagus Muscularis	GTEx
rs10800435	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs10800435	NME7	cis	Thyroid	GTEx
rs10800435	NME7	cis	Artery Tibial	GTEx
rs10800435	NME7	cis	Stomach	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:169296600-169324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
4	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:169309400-169336400	Weak transcription	Ovary	ovary
6	chr1:169310800-169332800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:169316000-169334200	Weak transcription	Fetal Intestine Small	intestine
9	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
10	chr1:169317200-169333800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:169317800-169332800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:169317800-169333800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:169317800-169335800	Weak transcription	Fetal Lung	lung
14	chr1:169318000-169332200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:169318200-169334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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