Variant report

Variant	rs10800439
Chromosome Location	chr1:169331039-169331040
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169327940..169332501-chr1:169336019..169339615,5	K562	blood:
2	chr1:169075705..169078397-chr1:169329097..169333069,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction
ENSG00000117475	Chromatin interaction
ENSG00000143156	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10458395	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10458396	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10458397	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800435	0.82[CEU][hapmap]
rs10800438	0.86[CEU][hapmap]
rs10800440	0.85[CEU][hapmap]
rs10800441	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800446	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919154	0.94[ASN][1000 genomes]
rs10919164	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919167	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1112839	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11800843	0.86[CHB][hapmap]
rs12022776	0.93[ASN][1000 genomes]
rs12023892	0.81[ASN][1000 genomes]
rs12024897	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12026287	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12026996	0.86[CHB][hapmap]
rs12027242	0.84[ASN][1000 genomes]
rs12029853	0.86[CHB][hapmap]
rs12030320	0.86[CHB][hapmap]
rs12033253	0.86[CHB][hapmap]
rs12034986	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12037211	0.86[CHB][hapmap]
rs12038609	0.86[CHB][hapmap]
rs12043489	0.86[CHB][hapmap]
rs12563090	0.88[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12564884	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1400838	0.81[ASN][1000 genomes]
rs1415928	0.86[CHB][hapmap]
rs1517748	1.00[ASN][1000 genomes]
rs1589113	0.86[CHB][hapmap]
rs16862172	0.86[CHB][hapmap]
rs1980198	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003652	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003654	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2014061	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2176473	0.85[CEU][hapmap]
rs2235195	0.86[CHB][hapmap]
rs2268048	0.86[CHB][hapmap]
rs2275299	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753303	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766089	0.86[CHB][hapmap]
rs3766096	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818844	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656670	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427186	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427188	0.89[ASN][1000 genomes]
rs6427189	0.90[ASN][1000 genomes]
rs6660945	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6669741	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6677410	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696428	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6696810	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72702156	0.81[ASN][1000 genomes]
rs7415756	0.85[CEU][hapmap]
rs7516248	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7528375	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528449	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534737	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537890	0.93[ASN][1000 genomes]
rs7539415	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs961404	0.82[AMR][1000 genomes];0.93[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	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	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
7	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3426048	chr1:169330775-169331261	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10800439	NME7	cis	Esophagus Muscularis	GTEx
rs10800439	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs10800439	NME7	cis	Nerve Tibial	GTEx
rs10800439	NME7	cis	Thyroid	GTEx
rs10800439	NME7	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
3	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:169309400-169336400	Weak transcription	Ovary	ovary
5	chr1:169310800-169332800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:169316000-169334200	Weak transcription	Fetal Intestine Small	intestine
8	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
9	chr1:169317200-169333800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:169317800-169332800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:169317800-169333800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:169317800-169335800	Weak transcription	Fetal Lung	lung
13	chr1:169318000-169332200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:169318200-169334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:169324600-169335800	Weak transcription	Primary T cells from cord blood	blood
16	chr1:169325000-169331800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:169325600-169331800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:169325600-169335800	Weak transcription	K562	blood
19	chr1:169326200-169334200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:169327200-169335800	Weak transcription	Small Intestine	intestine
21	chr1:169327200-169336200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:169328400-169332800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:169328800-169331800	Weak transcription	NHLF	lung
24	chr1:169329000-169331800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:169329800-169331200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:169329800-169332200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr1:169330000-169332600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:169330000-169336400	Weak transcription	Psoas Muscle	Psoas
29	chr1:169330200-169332800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:169330800-169331800	Weak transcription	NH-A	brain
31	chr1:169330800-169331800	Weak transcription	NHEK	skin
32	chr1:169330800-169335800	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:169330800-169336400	Weak transcription	Right Ventricle	heart
34	chr1:169331000-169332000	Weak transcription	GM12878-XiMat	blood
35	chr1:169331000-169332600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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