Variant report

Variant	rs10800424
Chromosome Location	chr1:169257424-169257425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1018831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10429893	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10732287	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10753785	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10753786	0.96[CEU][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs10800408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10800414	0.95[AMR][1000 genomes];0.93[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];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800435	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10800438	0.90[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	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10919124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919132	0.96[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs10919174	0.82[JPT][hapmap]
rs1200076	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1200077	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1200079	0.82[JPT][hapmap]
rs1200083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[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]
rs1200085	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]
rs1200161	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1200164	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1208135	0.82[JPT][hapmap]
rs1208327	0.81[ASN][1000 genomes]
rs1208370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1208371	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1208375	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1208377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12086665	0.82[JPT][hapmap]
rs12752748	0.82[JPT][hapmap]
rs1400836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1400839	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1517744	0.82[JPT][hapmap]
rs1517747	0.82[JPT][hapmap]
rs1591733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16861990	0.82[JPT][hapmap]
rs17345107	0.82[JPT][hapmap]
rs17349222	0.82[JPT][hapmap]
rs1829286	0.81[ASN][1000 genomes]
rs1829287	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1850525	0.81[EUR][1000 genomes]
rs1856303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1983546	0.82[JPT][hapmap]
rs2037250	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2066000	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2138898	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2152979	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2176473	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2176474	0.84[ASN][1000 genomes]
rs2211017	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2300158	0.96[CEU][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs2420008	0.82[JPT][hapmap]
rs3766057	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]
rs3766095	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs3905328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4264046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4300284	0.88[AMR][1000 genomes]
rs4454599	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4656183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs4656672	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6427185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs6656822	0.82[JPT][hapmap]
rs6662237	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6691226	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552323	0.82[JPT][hapmap]
rs994986	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1000254	chr1:169203554-169271792	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1009170	chr1:169207940-169270995	Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv508637	chr1:169214920-169268078	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1004674	chr1:169233962-169271792	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10800424	NME7	cis	Stomach	GTEx
rs10800424	NME7	cis	lung	GTEx
rs10800424	NME7	cis	Artery Aorta	GTEx
rs10800424	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs10800424	NME7	cis	Nerve Tibial	GTEx
rs10800424	NME7	cis	Esophagus Muscularis	GTEx
rs10800424	NME7	cis	Thyroid	GTEx
rs10800424	NME7	cis	Artery Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169251400-169271400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:169252800-169278600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:169252800-169278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:169253000-169264800	Weak transcription	Primary T cells from cord blood	blood
5	chr1:169253400-169270800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:169253600-169280600	Weak transcription	Fetal Kidney	kidney
7	chr1:169253800-169258200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:169254000-169274800	Weak transcription	Ovary	ovary
9	chr1:169254400-169263600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:169254800-169268600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:169254800-169281000	Weak transcription	Dnd41	blood
12	chr1:169255800-169264800	Weak transcription	Aorta	Aorta
13	chr1:169256200-169257800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:169256200-169257800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:169256200-169258000	Enhancers	HSMM	muscle
16	chr1:169256200-169258600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr1:169256200-169258800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr1:169256200-169259200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:169256400-169257600	Enhancers	NH-A	brain
20	chr1:169256400-169257800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:169256400-169257800	Enhancers	HSMMtube	muscle
22	chr1:169256400-169257800	Enhancers	HUVEC	blood vessel
23	chr1:169256400-169257800	Enhancers	Osteobl	bone
24	chr1:169256400-169258800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:169256400-169258800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:169256400-169258800	Enhancers	HMEC	breast
27	chr1:169256400-169258800	Enhancers	NHEK	skin
28	chr1:169256600-169258200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:169256600-169259600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:169256800-169257800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:169256800-169260200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:169256800-169271600	Weak transcription	Primary B cells from cord blood	blood
33	chr1:169256800-169278600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:169257200-169257600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:169257200-169257600	Enhancers	Placenta Amnion	Placenta Amnion
36	chr1:169257200-169257600	Enhancers	Hela-S3	cervix
37	chr1:169257200-169257800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:169257200-169257800	Flanking Active TSS	A549	lung
39	chr1:169257400-169257600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:169257400-169257800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:169257400-169257800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:169257400-169258600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:169257400-169258600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:169257400-169258800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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