Variant report

Variant	rs1200085
Chromosome Location	chr1:169137592-169137593
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	chr1:169132257..169133805-chr1:169136513..169138775,2	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732287	0.82[JPT][hapmap]
rs10753785	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753786	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs10800408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800414	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10800425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10800435	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10800438	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10800440	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919105	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10919132	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs1200076	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200077	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[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[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200161	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200164	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1208371	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1208375	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1208377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086665	0.82[JPT][hapmap]
rs12752748	0.82[JPT][hapmap]
rs1400839	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1591733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[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	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1856303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2037250	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066000	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2152979	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2176473	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2211017	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2300158	0.96[CEU][hapmap];0.90[YRI][hapmap]
rs2420008	0.82[JPT][hapmap]
rs3766057	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]
rs4264046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4454599	0.89[ASN][1000 genomes]
rs6662237	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6691226	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7415756	0.89[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7533257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7552323	0.82[JPT][hapmap]
rs994986	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AFR][1000 genomes];0.90[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
rs1200085	NME7	cis	Thyroid	GTEx
rs1200085	NME7	cis	Nerve Tibial	GTEx
rs1200085	NME7	cis	Artery Tibial	GTEx
rs1200085	NME7	cis	Stomach	GTEx
rs1200085	NME7	cis	Esophagus Muscularis	GTEx
rs1200085	NME7	cis	lung	GTEx
rs1200085	NME7	cis	Artery Aorta	GTEx
rs1200085	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
2	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:169116400-169139400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:169121000-169140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:169121200-169141200	Weak transcription	Left Ventricle	heart
7	chr1:169121800-169143000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:169124800-169138800	Weak transcription	Primary B cells from cord blood	blood
9	chr1:169130400-169195200	Weak transcription	Pancreas	Pancrea
10	chr1:169131000-169138800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:169131000-169139000	Weak transcription	Fetal Intestine Small	intestine
12	chr1:169131400-169139000	Weak transcription	Ovary	ovary
13	chr1:169131400-169149400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:169131600-169137600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:169132800-169139000	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:169135600-169139800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:169136400-169138600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:169137000-169137600	Strong transcription	Primary T cells from cord blood	blood
19	chr1:169137000-169138000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:169137200-169137600	Weak transcription	Psoas Muscle	Psoas
21	chr1:169137200-169137800	Enhancers	Stomach Mucosa	stomach
22	chr1:169137200-169138000	Enhancers	Sigmoid Colon	Sigmoid Colon

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