Variant report

Variant	rs994986
Chromosome Location	chr1:169289723-169289724
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169285804..169288205-chr1:169289257..169290945,2	MCF-7	breast:
2	chr1:169284485..169288949-chr1:169289510..169292758,5	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1018831	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10429893	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10732287	0.81[ASN][1000 genomes]
rs10753785	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10753786	0.89[EUR][1000 genomes]
rs10800408	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10800414	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10800424	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800425	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800435	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes]
rs10800438	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10800440	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10919105	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919124	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919132	0.88[EUR][1000 genomes]
rs1200076	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1200077	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1200083	1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1200085	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1200161	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1200164	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1208327	0.81[ASN][1000 genomes]
rs1208370	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1208371	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1208375	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1208377	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1400836	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1400839	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591733	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17516734	1.00[CHB][hapmap]
rs17576071	1.00[CHB][hapmap]
rs17577345	1.00[CHB][hapmap]
rs1829286	0.81[ASN][1000 genomes]
rs1829287	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1850525	0.83[EUR][1000 genomes]
rs1856303	1.00[CHB][hapmap];0.82[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037250	1.00[CHB][hapmap];0.82[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066000	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138898	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2152979	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176473	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2176474	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2211017	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300158	0.88[EUR][1000 genomes]
rs3766057	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766095	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3905328	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4264046	1.00[CHB][hapmap];0.82[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300284	0.81[AMR][1000 genomes]
rs4454599	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656183	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4656672	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6427185	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6662237	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691226	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7415756	0.82[JPT][hapmap]
rs7533257	1.00[CHB][hapmap];0.82[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
rs994986	NME7	cis	Thyroid	GTEx
rs994986	NME7	cis	Stomach	GTEx
rs994986	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs994986	NME7	cis	Nerve Tibial	GTEx
rs994986	NME7	cis	Artery Tibial	GTEx
rs994986	NME7	cis	Artery Aorta	GTEx
rs994986	NME7	cis	Esophagus Muscularis	GTEx
rs994986	NME7	cis	multi-tissue	Pritchard
rs994986	NME7	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169259600-169294400	Weak transcription	Pancreas	Pancrea
2	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
3	chr1:169264400-169294400	Weak transcription	Left Ventricle	heart
4	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
5	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:169271800-169297200	Weak transcription	Psoas Muscle	Psoas
7	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:169276800-169304600	Weak transcription	Ovary	ovary
9	chr1:169277000-169294600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:169277000-169306200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:169279000-169291200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:169279000-169293800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:169279000-169295600	Weak transcription	Adipose Nuclei	Adipose
14	chr1:169279200-169296000	Weak transcription	Primary T cells from cord blood	blood
15	chr1:169280200-169304600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:169281600-169294400	Weak transcription	Fetal Intestine Small	intestine
17	chr1:169281600-169294400	Weak transcription	Lung	lung
18	chr1:169281600-169306600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:169281800-169295400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:169282000-169290600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:169282000-169293800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:169282000-169294600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:169282000-169306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:169282200-169293600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:169282200-169295800	Weak transcription	NHEK	skin
26	chr1:169282400-169295600	Weak transcription	NH-A	brain
27	chr1:169283000-169290400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:169283400-169293400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:169286200-169290600	Weak transcription	Hela-S3	cervix
30	chr1:169286200-169295400	Weak transcription	HUVEC	blood vessel
31	chr1:169287400-169294400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:169288600-169297200	Weak transcription	Small Intestine	intestine
33	chr1:169288800-169290800	Weak transcription	NHDF-Ad	bronchial
34	chr1:169289200-169290800	Weak transcription	A549	lung
35	chr1:169289400-169290400	Weak transcription	Muscle Satellite Cultured Cells	--

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