Variant report

Variant	rs2176474
Chromosome Location	chr1:169313678-169313679
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10429893	0.82[AMR][1000 genomes]
rs10465575	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10800424	0.84[ASN][1000 genomes]
rs10800425	0.84[ASN][1000 genomes]
rs10800435	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800438	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10800440	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10919105	0.84[ASN][1000 genomes]
rs10919124	0.84[ASN][1000 genomes]
rs1200063	0.81[ASN][1000 genomes]
rs12029566	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1400839	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1591733	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1829287	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1856303	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2037250	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2066000	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2152979	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2176473	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2211017	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3905328	0.82[AMR][1000 genomes]
rs4264046	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4454599	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4656672	0.82[AMR][1000 genomes]
rs6662237	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6669901	0.81[AMR][1000 genomes]
rs6686204	0.88[EUR][1000 genomes]
rs6691226	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7415756	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7533257	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs925892	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs994986	0.84[AMR][1000 genomes];0.89[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2176474	NME7	cis	Nerve Tibial	GTEx
rs2176474	NME7	cis	Esophagus Muscularis	GTEx
rs2176474	NME7	cis	multi-tissue	Pritchard
rs2176474	NME7	cis	Stomach	GTEx
rs2176474	NME7	cis	Artery Tibial	GTEx
rs2176474	NME7	cis	Thyroid	GTEx
rs2176474	NME7	cis	Artery Aorta	GTEx
rs2176474	NME7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
2	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:169296600-169324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:169303800-169317600	Weak transcription	Liver	Liver
5	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
6	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:169309400-169314600	Weak transcription	K562	blood
8	chr1:169309400-169336400	Weak transcription	Ovary	ovary
9	chr1:169310600-169316800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:169310800-169332800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:169311200-169315800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:169311400-169314600	Weak transcription	Fetal Intestine Small	intestine
14	chr1:169311600-169314600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:169313600-169317000	Enhancers	Fetal Intestine Large	intestine

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