Variant report

Variant	rs1014965
Chromosome Location	chr1:169366076-169366077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10442644	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs12116551	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs12118611	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs12119479	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12121891	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12124049	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12128350	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs12140572	0.82[CEU][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes]
rs12143708	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12730053	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12750775	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12758228	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17349579	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs17577184	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1936533	0.85[YRI][hapmap]
rs2157597	0.81[CEU][hapmap];0.85[YRI][hapmap]
rs35010461	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35107735	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35220898	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs4589164	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs4656182	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4656664	0.85[YRI][hapmap]
rs4656671	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4656674	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4656677	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4656678	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4656680	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61806989	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61807017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6427193	0.85[CEU][hapmap]
rs6656463	0.80[CEU][hapmap]
rs6692649	0.95[CEU][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs722145	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7368145	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7516097	0.85[YRI][hapmap]
rs7522896	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7527703	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7542751	1.00[CEU][hapmap]
rs7546347	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1014965	NME7	cis	Artery Tibial	GTEx
rs1014965	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:169341200-169367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:169345800-169366400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:169349400-169367400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:169350200-169366800	Weak transcription	HSMMtube	muscle
6	chr1:169350200-169368600	Weak transcription	Colonic Mucosa	Colon
7	chr1:169352800-169367400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:169353000-169369800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:169354000-169370000	Weak transcription	Aorta	Aorta
10	chr1:169354800-169370600	Weak transcription	Fetal Kidney	kidney
11	chr1:169357000-169368200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:169358200-169368000	Weak transcription	Esophagus	oesophagus
13	chr1:169359200-169366800	Weak transcription	Fetal Brain Male	brain
14	chr1:169359200-169368400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:169359600-169369800	Weak transcription	NHDF-Ad	bronchial
16	chr1:169360600-169366200	Weak transcription	A549	lung
17	chr1:169360600-169372200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:169360800-169366200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:169360800-169367400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:169360800-169367800	Weak transcription	Psoas Muscle	Psoas
21	chr1:169360800-169369200	Weak transcription	Fetal Intestine Small	intestine
22	chr1:169360800-169370600	Weak transcription	NHLF	lung
23	chr1:169360800-169395200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:169361000-169366600	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:169361200-169366800	Weak transcription	Hela-S3	cervix
26	chr1:169361400-169368000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:169361400-169369400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:169361800-169366800	Weak transcription	Brain Substantia Nigra	brain
29	chr1:169362200-169367000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:169362200-169367400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:169362200-169370000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:169362200-169370000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:169362200-169371200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:169362400-169366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:169362400-169368000	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:169362400-169368800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:169362400-169369800	Weak transcription	Fetal Thymus	thymus
38	chr1:169362400-169370000	Weak transcription	Brain Germinal Matrix	brain
39	chr1:169362400-169370000	Weak transcription	Fetal Brain Female	brain
40	chr1:169362600-169369600	Weak transcription	Primary T cells from cord blood	blood
41	chr1:169363000-169366200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:169363200-169366200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:169363200-169368200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:169363400-169366200	Strong transcription	Liver	Liver
45	chr1:169363400-169368800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:169363400-169371200	Weak transcription	Ovary	ovary
47	chr1:169363600-169367800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:169363600-169368800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:169363800-169367000	Weak transcription	NHEK	skin
50	chr1:169363800-169367400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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