Variant report

Variant	rs12125650
Chromosome Location	chr1:150760174-150760175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150753935..150755523-chr1:150760046..150761556,2	MCF-7	breast:
2	chr1:150759798..150761774-chr1:150772351..150774481,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224690	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1081512	0.84[EUR][1000 genomes]
rs11204693	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap]
rs11204695	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap]
rs11204725	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11204737	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1136774	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126004	0.84[EUR][1000 genomes]
rs12402006	0.83[EUR][1000 genomes]
rs12404199	0.83[EUR][1000 genomes]
rs12410050	0.84[EUR][1000 genomes]
rs12568757	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12725806	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12758227	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16841689	0.82[YRI][hapmap]
rs17599629	0.91[YRI][hapmap]
rs2039590	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2089081	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs267733	0.91[YRI][hapmap]
rs34002273	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3754211	1.00[CEU][hapmap];0.95[TSI][hapmap]
rs486836	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4970924	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap]
rs4970926	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap]
rs4970932	0.80[EUR][1000 genomes]
rs4970976	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587520	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6694531	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap]
rs7520022	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap]
rs7534124	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9733	0.88[ASW][hapmap];0.89[CEU][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap]

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	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	esv1831388	chr1:150753239-150760996	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv2788	chr1:150755334-150800785	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:33)

SNP	Gene	Cis/trans	Tissue	Source
rs12125650	ARNT	cis	parietal	SCAN
rs12125650	CTSS	cis	cerebellum	SCAN
rs12125650	FLG	cis	cerebellum	SCAN
rs12125650	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs12125650	RP11-316M1.12	cis	Thyroid	GTEx
rs12125650	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs12125650	CTSS	cis	lymphoblastoid	seeQTL
rs12125650	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs12125650	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs12125650	MCL1	cis	cerebellum	SCAN
rs12125650	RP11-316M1.12	cis	Whole Blood	GTEx
rs12125650	CTSS	cis	Thyroid	GTEx
rs12125650	FMO5	cis	cerebellum	SCAN
rs12125650	RP11-316M1.12	cis	lung	GTEx
rs12125650	HORMAD1	cis	parietal	SCAN
rs12125650	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs12125650	CTSK	cis	lymphoblastoid	seeQTL
rs12125650	CTSK	cis	parietal	SCAN
rs12125650	HORMAD1	cis	Nerve Tibial	GTEx
rs12125650	RP11-316M1.12	cis	Artery Tibial	GTEx
rs12125650	CTSK	cis	cerebellum	SCAN
rs12125650	PSMD4	cis	parietal	SCAN
rs12125650	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs12125650	CTSK	cis	multi-tissue	Pritchard
rs12125650	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs12125650	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs12125650	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs12125650	CTSS	cis	parietal	SCAN
rs12125650	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs12125650	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs12125650	CTSS	cis	multi-tissue	Pritchard
rs12125650	HORMAD1	cis	Esophagus Mucosa	GTEx
rs12125650	ARNT	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150737200-150761800	Weak transcription	Spleen	Spleen
2	chr1:150744600-150768200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:150750600-150767600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:150756200-150766800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:150756400-150767600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:150756600-150760200	Weak transcription	Ovary	ovary
7	chr1:150758000-150763800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:150758800-150768400	Weak transcription	Brain Germinal Matrix	brain
9	chr1:150759400-150760400	Weak transcription	Colonic Mucosa	Colon
10	chr1:150759600-150760200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:150759600-150760200	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr1:150759800-150760200	Enhancers	Primary B cells from cord blood	blood
13	chr1:150759800-150760600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:150759800-150764800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr1:150760000-150760200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:150760000-150760200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:150760000-150760600	Enhancers	K562	blood
18	chr1:150760000-150760800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:150760000-150761200	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links