Variant report

Variant	rs10919144
Chromosome Location	chr1:169308424-169308425
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1011638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1018832	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10442644	0.82[CEU][hapmap]
rs10458394	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10489417	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10494477	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10494478	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10737545	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800423	0.86[EUR][1000 genomes]
rs10800429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800433	1.00[ASN][1000 genomes]
rs10800434	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919085	1.00[JPT][hapmap]
rs10919125	1.00[ASN][1000 genomes]
rs10919127	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10919128	1.00[ASN][1000 genomes]
rs10919130	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919133	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919134	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919135	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919147	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10919158	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12022617	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12025566	1.00[JPT][hapmap]
rs12028208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12029800	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12029857	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12030541	1.00[ASN][1000 genomes]
rs12030810	1.00[ASN][1000 genomes]
rs12031371	1.00[ASN][1000 genomes]
rs12031830	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036426	1.00[ASN][1000 genomes]
rs12042082	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12042990	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12045803	1.00[ASN][1000 genomes]
rs12118611	0.82[CEU][hapmap]
rs12405725	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12567342	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1517749	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517750	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345156	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17345426	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[ASN][1000 genomes]
rs17518147	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1856302	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2090514	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157597	0.82[CEU][hapmap]
rs2179491	0.86[CEU][hapmap]
rs35220898	0.82[CEU][hapmap]
rs3766074	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4497270	0.81[ASN][1000 genomes]
rs4534447	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4562680	0.86[ASN][1000 genomes]
rs4589164	0.82[CEU][hapmap]
rs61806987	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413522	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522565	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7528142	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7556463	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs929132	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929133	0.87[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs9887925	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10919144	NME7	cis	Thyroid	GTEx
rs10919144	NME7	cis	Artery Tibial	GTEx
rs10919144	NME7	cis	cerebellum	SCAN
rs10919144	NME7	cis	Esophagus Muscularis	GTEx
rs10919144	NME7	cis	lymphoblastoid	seeQTL
rs10919144	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs10919144	ALDH9A1	cis	cerebellum	SCAN
rs10919144	NME7	cis	Nerve Tibial	GTEx
rs10919144	NME7	cis	Esophagus Mucosa	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
2	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
3	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:169291000-169313200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:169296600-169310400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:169296600-169324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:169303000-169312600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:169303800-169317600	Weak transcription	Liver	Liver
10	chr1:169304800-169313200	Weak transcription	Spleen	Spleen
11	chr1:169305400-169308800	Weak transcription	Ovary	ovary
12	chr1:169305600-169312400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
14	chr1:169306600-169309000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:169306600-169309200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:169306800-169309200	Enhancers	Primary hematopoietic stem cells	blood
17	chr1:169306800-169310400	Weak transcription	Fetal Intestine Large	intestine
18	chr1:169307000-169310400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:169307000-169310400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:169307600-169309000	Enhancers	Dnd41	blood
21	chr1:169307600-169309400	Enhancers	K562	blood
22	chr1:169308000-169311200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:169308200-169309400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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