Variant report

Variant	rs10919132
Chromosome Location	chr1:169280253-169280254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10158131	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs1018831	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs10753785	0.81[EUR][1000 genomes]
rs10753786	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800408	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs10800414	0.81[EUR][1000 genomes]
rs10800424	0.96[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs10800425	0.96[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs10800435	0.82[CEU][hapmap];0.93[YRI][hapmap]
rs10800438	0.85[CEU][hapmap];0.92[YRI][hapmap]
rs10800440	0.85[CEU][hapmap]
rs10800447	0.94[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs10919105	0.82[EUR][1000 genomes]
rs10919124	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs10919136	0.89[ASN][1000 genomes]
rs10919140	0.88[CHB][hapmap];0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs10919141	0.83[ASN][1000 genomes]
rs10919148	0.85[ASN][1000 genomes]
rs10919173	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs1200076	0.81[EUR][1000 genomes]
rs1200077	0.81[EUR][1000 genomes]
rs1200083	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs1200085	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs1208370	0.96[CEU][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs1208371	0.81[EUR][1000 genomes]
rs1208375	0.81[EUR][1000 genomes]
rs1208377	0.96[CEU][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs12733037	0.82[CHB][hapmap]
rs1400836	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs1400839	0.88[EUR][1000 genomes]
rs1517745	0.88[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs1591733	0.96[CEU][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs16862217	0.81[CHB][hapmap]
rs1829287	0.85[EUR][1000 genomes]
rs1850525	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1856303	0.96[CEU][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes]
rs1980198	0.82[MEX][hapmap]
rs2037250	0.92[CEU][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs2066000	0.88[EUR][1000 genomes]
rs2152979	0.88[EUR][1000 genomes]
rs2176473	0.85[CEU][hapmap];0.93[YRI][hapmap]
rs2211017	0.88[EUR][1000 genomes]
rs2275299	0.82[MEX][hapmap]
rs2300157	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs2300158	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766057	0.96[CEU][hapmap]
rs3766095	0.89[YRI][hapmap]
rs3905328	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs4264046	0.96[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs4529780	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656183	0.89[YRI][hapmap]
rs4656670	0.82[MEX][hapmap]
rs6427185	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs6662237	0.87[EUR][1000 genomes]
rs6672589	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs6686204	0.95[ASN][1000 genomes]
rs6691226	0.88[EUR][1000 genomes]
rs7415756	0.85[CEU][hapmap];0.96[YRI][hapmap]
rs7533257	0.96[CEU][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs994986	0.88[EUR][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10919132	C1orf114	cis	cerebellum	SCAN
rs10919132	NME7	cis	Thyroid	GTEx
rs10919132	SCYL3	cis	parietal	SCAN
rs10919132	NME7	cis	Nerve Tibial	GTEx
rs10919132	NME7	cis	Esophagus Muscularis	GTEx
rs10919132	SELP	cis	cerebellum	SCAN
rs10919132	NME7	cis	multi-tissue	Pritchard
rs10919132	TAC1	trans	cerebellum	SCAN
rs10919132	F5	cis	cerebellum	SCAN
rs10919132	NME7	cis	Artery Tibial	GTEx
rs10919132	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs10919132	NME7	cis	Stomach	GTEx
rs10919132	NME7	cis	lymphoblastoid	seeQTL
rs10919132	NME7	cis	lung	GTEx

Chromatin state (count:56 , 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	chr1:169267000-169281200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:169267800-169281200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:169269000-169281200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:169269200-169281400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:169269400-169281600	Weak transcription	HUVEC	blood vessel
18	chr1:169269600-169281000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:169271800-169297200	Weak transcription	Psoas Muscle	Psoas
21	chr1:169273600-169281000	Weak transcription	A549	lung
22	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:169275200-169281400	Weak transcription	Fetal Thymus	thymus
24	chr1:169275600-169280400	Weak transcription	Fetal Lung	lung
25	chr1:169275600-169281200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:169276400-169281200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:169276400-169281200	Weak transcription	NH-A	brain
28	chr1:169276400-169281400	Weak transcription	HSMMtube	muscle
29	chr1:169276800-169304600	Weak transcription	Ovary	ovary
30	chr1:169277000-169281200	Weak transcription	HSMM	muscle
31	chr1:169277000-169294600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:169277000-169306200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:169278000-169285800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:169279000-169281200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:169279000-169281200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:169279000-169281400	Weak transcription	Primary B cells from cord blood	blood
37	chr1:169279000-169281400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:169279000-169281400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:169279000-169282000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:169279000-169288400	Weak transcription	Brain Angular Gyrus	brain
41	chr1:169279000-169291200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:169279000-169293800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:169279000-169295600	Weak transcription	Adipose Nuclei	Adipose
44	chr1:169279200-169281200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr1:169279200-169281400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:169279200-169281400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:169279200-169282000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr1:169279200-169287200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:169279200-169296000	Weak transcription	Primary T cells from cord blood	blood
50	chr1:169279400-169281600	Weak transcription	Monocytes-CD14+_RO01746	blood

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