Variant report

Variant	rs925892
Chromosome Location	chr1:169335254-169335255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169324847..169326824-chr1:169332989..169335675,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10429893	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465575	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465576	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489189	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800435	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10800438	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800440	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919168	0.81[ASN][1000 genomes]
rs1124843	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133814	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029566	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076993	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208134	0.81[ASN][1000 genomes]
rs1208135	0.81[ASN][1000 genomes]
rs1400836	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517744	0.81[ASN][1000 genomes]
rs1517747	0.81[ASN][1000 genomes]
rs1914505	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003653	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138898	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176473	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176474	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3820059	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905328	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656183	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656672	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427187	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669901	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700375	0.81[ASN][1000 genomes]
rs7415756	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535765	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7544221	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554689	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs760603	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932301	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs925892	NME7	cis	Thyroid	GTEx
rs925892	NME7	cis	Artery Tibial	GTEx
rs925892	NME7	cis	Esophagus Muscularis	GTEx
rs925892	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

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	chr1:169309400-169336400	Weak transcription	Ovary	ovary
4	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
6	chr1:169317800-169335800	Weak transcription	Fetal Lung	lung
7	chr1:169324600-169335800	Weak transcription	Primary T cells from cord blood	blood
8	chr1:169325600-169335800	Weak transcription	K562	blood
9	chr1:169327200-169335800	Weak transcription	Small Intestine	intestine
10	chr1:169327200-169336200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:169330000-169336400	Weak transcription	Psoas Muscle	Psoas
12	chr1:169330800-169335800	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:169330800-169336400	Weak transcription	Right Ventricle	heart
14	chr1:169331400-169335800	Weak transcription	Fetal Intestine Large	intestine
15	chr1:169331600-169335600	Enhancers	HMEC	breast
16	chr1:169331800-169335800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:169331800-169336200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:169332000-169335800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:169332200-169336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:169332800-169336400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:169333000-169336000	Weak transcription	NHDF-Ad	bronchial
22	chr1:169333000-169336200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:169333000-169336200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:169333000-169336200	Weak transcription	Thymus	Thymus
25	chr1:169333200-169335800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:169333200-169335800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:169333200-169335800	Weak transcription	NHLF	lung
28	chr1:169333200-169336000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:169333200-169336200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr1:169333200-169336200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:169333200-169336200	Weak transcription	Fetal Stomach	stomach
32	chr1:169333200-169336200	Enhancers	Hela-S3	cervix
33	chr1:169333200-169336400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:169333200-169336400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:169333400-169335800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:169333400-169335800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:169333400-169335800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:169333400-169336000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:169333400-169336000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:169333400-169336000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:169333400-169336000	Weak transcription	HUVEC	blood vessel
42	chr1:169333400-169336200	Weak transcription	Osteobl	bone
43	chr1:169333600-169335600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:169333600-169335600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:169333600-169335800	Weak transcription	NH-A	brain
46	chr1:169334000-169336000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:169334200-169335800	Weak transcription	Brain Anterior Caudate	brain
48	chr1:169334200-169335800	Weak transcription	Fetal Brain Female	brain
49	chr1:169334200-169336000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:169334200-169336400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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