Variant report

Variant	rs1011638
Chromosome Location	chr1:169279707-169279708
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	chr1:169073990..169076920-chr1:169277266..169279793,2	K562	blood:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1018832	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10442644	0.82[CEU][hapmap]
rs10458394	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10489417	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10494477	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10494478	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10737545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800423	0.87[EUR][1000 genomes]
rs10800429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800433	1.00[ASN][1000 genomes]
rs10800434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919062	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10919070	1.00[JPT][hapmap]
rs10919071	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10919085	1.00[JPT][hapmap]
rs10919125	1.00[ASN][1000 genomes]
rs10919127	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10919128	1.00[ASN][1000 genomes]
rs10919130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919133	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919134	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919147	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10919158	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12022617	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12025566	1.00[JPT][hapmap]
rs12028208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12029800	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12029857	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12030541	1.00[ASN][1000 genomes]
rs12030810	1.00[ASN][1000 genomes]
rs12031371	1.00[ASN][1000 genomes]
rs12031830	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035622	1.00[JPT][hapmap]
rs12036426	1.00[ASN][1000 genomes]
rs12042082	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12042990	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12045803	1.00[ASN][1000 genomes]
rs12118611	0.82[CEU][hapmap]
rs12405725	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12567342	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1517749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345156	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17345426	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[ASN][1000 genomes]
rs17518147	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1856302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2000321	1.00[JPT][hapmap]
rs2090514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143290	1.00[JPT][hapmap]
rs2157597	0.82[CEU][hapmap]
rs2179491	0.86[CEU][hapmap]
rs35220898	0.82[CEU][hapmap]
rs3766074	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4497270	0.81[ASN][1000 genomes]
rs4534447	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4562680	0.86[ASN][1000 genomes]
rs4589164	0.82[CEU][hapmap]
rs61806987	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522565	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7528142	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7556463	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs929132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929133	0.87[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs9887925	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1011638	NME7	cis	Thyroid	GTEx
rs1011638	NME7	cis	Esophagus Mucosa	GTEx
rs1011638	NME7	cis	multi-tissue	Pritchard
rs1011638	NME7	cis	Nerve Tibial	GTEx
rs1011638	NME7	cis	Artery Tibial	GTEx
rs1011638	NME7	cis	Esophagus Muscularis	GTEx
rs1011638	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169253600-169280600	Weak transcription	Fetal Kidney	kidney
2	chr1:169254800-169281000	Weak transcription	Dnd41	blood
3	chr1:169257600-169284800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:169257800-169281200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:169259600-169294400	Weak transcription	Pancreas	Pancrea
6	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
7	chr1:169264000-169281400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:169264400-169294400	Weak transcription	Left Ventricle	heart
9	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
10	chr1:169265200-169281200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:169265400-169281200	Weak transcription	NHDF-Ad	bronchial
12	chr1:169265800-169281000	Weak transcription	Fetal Intestine Large	intestine
13	chr1:169266200-169280200	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:169267000-169281200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:169267800-169281200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:169269000-169281200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:169269200-169281400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:169269400-169281600	Weak transcription	HUVEC	blood vessel
19	chr1:169269600-169281000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:169271800-169297200	Weak transcription	Psoas Muscle	Psoas
22	chr1:169273600-169281000	Weak transcription	A549	lung
23	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:169273800-169279800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:169275200-169281400	Weak transcription	Fetal Thymus	thymus
26	chr1:169275600-169280400	Weak transcription	Fetal Lung	lung
27	chr1:169275600-169281200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:169276400-169281200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:169276400-169281200	Weak transcription	NH-A	brain
30	chr1:169276400-169281400	Weak transcription	HSMMtube	muscle
31	chr1:169276800-169304600	Weak transcription	Ovary	ovary
32	chr1:169277000-169281200	Weak transcription	HSMM	muscle
33	chr1:169277000-169294600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:169277000-169306200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:169277800-169280000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:169278000-169285800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:169278200-169279800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:169279000-169281200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:169279000-169281200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:169279000-169281400	Weak transcription	Primary B cells from cord blood	blood
41	chr1:169279000-169281400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:169279000-169281400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:169279000-169282000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:169279000-169288400	Weak transcription	Brain Angular Gyrus	brain
45	chr1:169279000-169291200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:169279000-169293800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:169279000-169295600	Weak transcription	Adipose Nuclei	Adipose
48	chr1:169279200-169279800	Weak transcription	Brain Germinal Matrix	brain
49	chr1:169279200-169280200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:169279200-169281200	Weak transcription	Primary monocytes fromperipheralblood	blood

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