Variant report

Variant	rs3766057
Chromosome Location	chr1:169135429-169135430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169124501..169127273-chr1:169133900..169136216,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1018831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732287	0.82[JPT][hapmap]
rs10753785	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753786	0.96[CEU][hapmap]
rs10800408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800414	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10800425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10800435	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10800438	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10800440	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919105	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10919132	0.96[CEU][hapmap]
rs1200076	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200077	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200079	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1200083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200161	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200164	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1208371	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1208375	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1208377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086665	0.82[JPT][hapmap]
rs12752748	0.82[JPT][hapmap]
rs1400839	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1591733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16861990	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs17345107	0.82[JPT][hapmap]
rs17349222	0.82[JPT][hapmap]
rs1829287	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1856303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2037250	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066000	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2152979	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2176473	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2211017	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2300158	0.96[CEU][hapmap]
rs2420008	0.82[JPT][hapmap]
rs4264046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4454599	0.89[ASN][1000 genomes]
rs6662237	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6691226	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7415756	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs7533257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7552323	0.82[JPT][hapmap]
rs994986	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3766057	NME7	cis	lung	GTEx
rs3766057	NME7	cis	multi-tissue	Pritchard
rs3766057	NME7	cis	Artery Tibial	GTEx
rs3766057	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs3766057	NME7	cis	Nerve Tibial	GTEx
rs3766057	NME7	cis	Esophagus Muscularis	GTEx
rs3766057	NME7	cis	Stomach	GTEx
rs3766057	NME7	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
2	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
3	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
5	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:169116400-169139400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:169118000-169137000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:169121000-169137000	Weak transcription	Psoas Muscle	Psoas
9	chr1:169121000-169140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:169121200-169141200	Weak transcription	Left Ventricle	heart
11	chr1:169121800-169143000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:169122800-169136400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:169124800-169138800	Weak transcription	Primary B cells from cord blood	blood
14	chr1:169127200-169137200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:169128200-169137000	Weak transcription	Aorta	Aorta
16	chr1:169130400-169195200	Weak transcription	Pancreas	Pancrea
17	chr1:169131000-169138800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:169131000-169139000	Weak transcription	Fetal Intestine Small	intestine
19	chr1:169131400-169139000	Weak transcription	Ovary	ovary
20	chr1:169131400-169149400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:169131600-169137600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:169132800-169139000	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:169133000-169137000	Weak transcription	A549	lung

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