Variant report

Variant	rs10800425
Chromosome Location	chr1:169258843-169258844
allele	A/G
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];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10429893	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10732287	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10753785	0.94[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];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10800414	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10800424	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	0.85[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	0.97[AFR][1000 genomes];0.96[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];0.99[AFR][1000 genomes];0.97[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	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1200077	0.89[AFR][1000 genomes];0.86[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];0.87[AFR][1000 genomes];0.81[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];0.87[AFR][1000 genomes];0.81[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	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];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1208371	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1208375	0.94[AFR][1000 genomes];0.94[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];0.94[AFR][1000 genomes];0.91[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];0.84[YRI][hapmap]
rs1400839	0.97[AFR][1000 genomes];0.91[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];0.99[AFR][1000 genomes];0.96[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	0.94[AFR][1000 genomes];0.96[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];0.97[AFR][1000 genomes];0.91[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];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2066000	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2138898	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2152979	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2176473	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2176474	0.84[ASN][1000 genomes]
rs2211017	0.99[AFR][1000 genomes];0.96[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];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3766095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs3905328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs4264046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4300284	0.89[AMR][1000 genomes]
rs4454599	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4656183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs4656672	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6427185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs6656822	0.82[JPT][hapmap]
rs6662237	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6691226	0.99[AFR][1000 genomes];0.96[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];0.97[AFR][1000 genomes];0.91[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];0.97[AFR][1000 genomes];0.91[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
rs10800425	NME7	cis	Nerve Tibial	GTEx
rs10800425	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs10800425	NME7	cis	Thyroid	GTEx
rs10800425	NME7	cis	Esophagus Muscularis	GTEx
rs10800425	NME7	cis	lung	GTEx
rs10800425	NME7	cis	Artery Aorta	GTEx
rs10800425	NME7	cis	Stomach	GTEx
rs10800425	NME7	cis	Artery Tibial	GTEx

Chromatin state (count:27 , 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	chr1:169254000-169274800	Weak transcription	Ovary	ovary
8	chr1:169254400-169263600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:169254800-169268600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:169254800-169281000	Weak transcription	Dnd41	blood
11	chr1:169255800-169264800	Weak transcription	Aorta	Aorta
12	chr1:169256200-169259200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:169256600-169259600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:169256800-169260200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:169256800-169271600	Weak transcription	Primary B cells from cord blood	blood
16	chr1:169256800-169278600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:169257600-169268600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:169257600-169284800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:169257800-169263400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:169257800-169281200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:169258600-169271200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:169258600-169276400	Weak transcription	HSMM	muscle
23	chr1:169258800-169263600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:169258800-169264000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:169258800-169264200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:169258800-169274600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:169258800-169277400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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