Variant report

Variant	rs12022617
Chromosome Location	chr1:169339884-169339885
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169073561..169077593-chr1:169336088..169341683,7	K562	blood:
2	chr1:169338121..169342264-chr1:169451874..169455112,4	K562	blood:
3	chr1:169337259..169338842-chr1:169338923..169340546,3	MCF-7	breast:
4	chr1:169338197..169339910-chr1:169345261..169347920,2	MCF-7	breast:
5	chr1:169275275..169277238-chr1:169338409..169341241,2	K562	blood:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction
ENSG00000117475	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1011638	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1018832	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10458394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs10489190	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs10494477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10494478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800429	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10800431	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10800432	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10800433	1.00[AFR][1000 genomes]
rs10919085	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10919122	1.00[AFR][1000 genomes]
rs10919123	1.00[AFR][1000 genomes]
rs10919125	1.00[AFR][1000 genomes]
rs10919127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs10919144	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10919149	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919150	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919162	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919165	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919172	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12021696	1.00[AFR][1000 genomes]
rs12022768	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12025397	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12025566	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12025721	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028197	1.00[AFR][1000 genomes]
rs12028208	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12029800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12029857	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12030541	1.00[AFR][1000 genomes]
rs12030810	1.00[AFR][1000 genomes]
rs12031371	1.00[AFR][1000 genomes]
rs12036426	1.00[AFR][1000 genomes]
rs12037926	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12042990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12044982	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045803	1.00[AFR][1000 genomes]
rs12048188	1.00[AFR][1000 genomes]
rs12401962	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401966	1.00[AFR][1000 genomes]
rs12402774	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12405185	1.00[AFR][1000 genomes]
rs12405725	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs12408636	1.00[AFR][1000 genomes]
rs12410241	1.00[AFR][1000 genomes]
rs12410387	1.00[AFR][1000 genomes]
rs12410456	1.00[AFR][1000 genomes]
rs12567342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1517742	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1517746	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17345426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17345531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17349677	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518147	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17576927	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1949426	1.00[ASN][1000 genomes]
rs2001156	1.00[AFR][1000 genomes]
rs2092083	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34323371	1.00[AFR][1000 genomes]
rs3766074	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs3766100	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766101	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4497270	1.00[AFR][1000 genomes]
rs4562680	1.00[AFR][1000 genomes]
rs72704035	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72706084	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7413522	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7414819	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7522565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7528142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7546361	0.93[ASN][1000 genomes]
rs7554853	1.00[ASN][1000 genomes]
rs7556463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12022617	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338000-169340000	Weak transcription	Left Ventricle	heart
2	chr1:169338000-169351200	Weak transcription	Lung	lung
3	chr1:169338000-169351200	Weak transcription	Spleen	Spleen
4	chr1:169338000-169353600	Weak transcription	Small Intestine	intestine
5	chr1:169338000-169358000	Weak transcription	Esophagus	oesophagus
6	chr1:169338000-169360000	Weak transcription	Fetal Heart	heart
7	chr1:169338000-169360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:169338000-169365200	Weak transcription	Gastric	stomach
9	chr1:169338000-169365600	Weak transcription	Pancreas	Pancrea
10	chr1:169338200-169340600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:169338200-169341200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:169338200-169341600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:169338200-169345800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:169338200-169345800	Weak transcription	Ovary	ovary
15	chr1:169338200-169351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:169338200-169360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:169338200-169360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:169338200-169362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:169338200-169363600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:169338200-169363600	Weak transcription	Stomach Mucosa	stomach
21	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:169338400-169345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:169338400-169345800	Weak transcription	Right Ventricle	heart
24	chr1:169338400-169349600	Weak transcription	HSMMtube	muscle
25	chr1:169338400-169360200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:169338400-169362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:169338600-169340400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:169338600-169341600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:169338600-169341800	Weak transcription	Fetal Kidney	kidney
30	chr1:169338600-169345800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:169338600-169345800	Weak transcription	Colonic Mucosa	Colon
32	chr1:169338600-169345800	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:169338600-169345800	Weak transcription	Psoas Muscle	Psoas
34	chr1:169338600-169346000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:169338600-169346000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:169338600-169349800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:169338600-169351400	Weak transcription	Thymus	Thymus
38	chr1:169338600-169352200	Weak transcription	Aorta	Aorta
39	chr1:169338600-169352200	Weak transcription	Fetal Stomach	stomach
40	chr1:169338600-169352400	Weak transcription	Fetal Intestine Small	intestine
41	chr1:169338600-169352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:169338600-169357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:169338800-169340200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:169338800-169340400	Genic enhancers	Primary T cells from cord blood	blood
45	chr1:169338800-169340800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:169338800-169341600	Weak transcription	Primary B cells from cord blood	blood
47	chr1:169338800-169345800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:169338800-169347400	Weak transcription	Fetal Brain Female	brain
49	chr1:169339000-169340400	Strong transcription	NH-A	brain
50	chr1:169339000-169340600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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