Variant report

Variant	rs6580738
Chromosome Location	chr12:50705715-50705716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr12:50705225-50706511	IMR90	lung:	n/a	n/a
2	RCOR1	chr12:50705557-50706424	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50614138..50615726-chr12:50704917..50707484,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196082	TF binding region
ENSG00000203424	TF binding region
ENSG00000050405	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs1044370	0.82[LWK][hapmap]
rs10506292	0.96[CEU][hapmap]
rs10783342	0.88[LWK][hapmap];0.81[MKK][hapmap]
rs10783344	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs10783349	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783350	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876013	0.86[EUR][1000 genomes]
rs10876014	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs10876015	0.96[CEU][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs10876016	0.93[EUR][1000 genomes]
rs10876017	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs10876018	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876023	0.96[CEU][hapmap]
rs10876024	0.96[CEU][hapmap]
rs10876027	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11169314	0.83[EUR][1000 genomes]
rs11169315	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs11169317	0.85[EUR][1000 genomes]
rs11169319	0.82[EUR][1000 genomes]
rs11169322	0.96[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs11169331	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs11169332	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs11169335	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs11169339	0.88[EUR][1000 genomes]
rs11169345	0.92[EUR][1000 genomes]
rs11169347	0.92[EUR][1000 genomes]
rs11169348	0.96[CEU][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs11169349	0.93[EUR][1000 genomes]
rs11169350	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs11169351	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs11169357	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs11169359	0.92[EUR][1000 genomes]
rs11169360	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs11169367	0.89[EUR][1000 genomes]
rs11169369	0.93[EUR][1000 genomes]
rs11169370	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs11169371	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169373	0.91[EUR][1000 genomes]
rs11169374	0.91[EUR][1000 genomes]
rs11169375	0.89[EUR][1000 genomes]
rs11169376	0.88[EUR][1000 genomes]
rs11169377	0.88[EUR][1000 genomes]
rs11169379	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169386	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11833608	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs11836169	0.89[EUR][1000 genomes]
rs11838347	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs12303082	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs12367872	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs12422417	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs12424691	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12424713	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs12425229	0.86[EUR][1000 genomes]
rs12425705	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12426444	0.84[EUR][1000 genomes]
rs12811291	0.86[EUR][1000 genomes]
rs12821454	0.92[EUR][1000 genomes]
rs12821504	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12823506	0.88[EUR][1000 genomes]
rs12828340	0.96[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs12832940	0.92[EUR][1000 genomes]
rs1362983	0.96[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs17124562	0.86[EUR][1000 genomes]
rs1972611	0.88[EUR][1000 genomes]
rs2111988	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs2302900	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2358539	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs28628775	0.92[EUR][1000 genomes]
rs34039674	0.88[EUR][1000 genomes]
rs34614542	0.89[EUR][1000 genomes]
rs34825838	0.84[EUR][1000 genomes]
rs34849043	0.90[EUR][1000 genomes]
rs34858415	0.89[EUR][1000 genomes]
rs35209607	0.91[EUR][1000 genomes]
rs35535298	0.91[EUR][1000 genomes]
rs35663729	0.85[EUR][1000 genomes]
rs35768991	0.87[EUR][1000 genomes]
rs35878271	0.88[EUR][1000 genomes]
rs35933908	0.93[EUR][1000 genomes]
rs3812825	0.96[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs3861100	0.84[EUR][1000 genomes]
rs4348979	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs4421818	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs4768872	0.88[EUR][1000 genomes]
rs4768949	0.88[EUR][1000 genomes]
rs4768951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6580729	0.82[LWK][hapmap]
rs6580735	0.92[EUR][1000 genomes]
rs6580736	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580737	0.93[EUR][1000 genomes]
rs6580739	0.89[EUR][1000 genomes]
rs6580740	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580741	0.88[EUR][1000 genomes]
rs67138019	0.91[EUR][1000 genomes]
rs7132551	0.96[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs7134595	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs7135777	0.92[EUR][1000 genomes]
rs7138420	0.92[CEU][hapmap]
rs7138622	0.92[CEU][hapmap]
rs71465002	0.86[EUR][1000 genomes]
rs7296291	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs7301186	0.83[EUR][1000 genomes]
rs7301189	0.82[EUR][1000 genomes]
rs7304445	0.92[EUR][1000 genomes]
rs7305995	0.92[EUR][1000 genomes]
rs7308095	0.83[EUR][1000 genomes]
rs7308885	0.86[EUR][1000 genomes]
rs7310541	0.89[EUR][1000 genomes]
rs7311378	0.92[EUR][1000 genomes]
rs7311491	0.92[EUR][1000 genomes]
rs7311973	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7312252	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs7314465	0.86[EUR][1000 genomes]
rs7315690	0.92[CEU][hapmap]
rs7315871	0.86[EUR][1000 genomes]
rs7315955	0.87[EUR][1000 genomes]
rs7399343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7485486	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7486747	0.96[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs7488682	0.93[EUR][1000 genomes]
rs7489214	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7953953	0.96[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs7956468	0.93[EUR][1000 genomes]
rs7967954	0.94[LWK][hapmap];0.81[MKK][hapmap]
rs7974648	0.87[EUR][1000 genomes]
rs7979830	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7980911	0.92[EUR][1000 genomes]
rs8181679	0.88[LWK][hapmap]
rs9705460	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv702	chr12:50670870-50715934	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv1053667	chr12:50679039-50801752	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6580738	EPLIN	cis	multi-tissue	Pritchard
rs6580738	CELA1	cis	parietal	SCAN
rs6580738	LASS5	cis	multi-tissue	Pritchard
rs6580738	LASS5	cis	parietal	SCAN
rs6580738	SLC38A1	cis	parietal	SCAN
rs6580738	LASS5	cis	cerebellum	SCAN
rs6580738	CERS5	cis	Nerve Tibial	GTEx
rs6580738	MCRS1	cis	parietal	SCAN
rs6580738	KIAA1463	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50678400-50708600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:50679800-50708600	Weak transcription	Liver	Liver
3	chr12:50690000-50711800	Weak transcription	Ovary	ovary
4	chr12:50692000-50719800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:50692400-50708800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:50693600-50722800	Weak transcription	Fetal Intestine Small	intestine
7	chr12:50697200-50707200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:50698200-50705800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:50698400-50705800	Weak transcription	A549	lung
10	chr12:50698800-50708600	Weak transcription	Hela-S3	cervix
11	chr12:50704400-50705800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:50704600-50707200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:50705000-50707800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:50705400-50707400	Enhancers	Osteobl	bone
15	chr12:50705400-50707600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:50705600-50706000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:50705600-50706000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr12:50705600-50706000	Enhancers	HSMM	muscle
19	chr12:50705600-50706000	Enhancers	HSMMtube	muscle
20	chr12:50705600-50706000	Enhancers	K562	blood
21	chr12:50705600-50706000	Enhancers	NHLF	lung
22	chr12:50705600-50706600	Enhancers	NHDF-Ad	bronchial
23	chr12:50705600-50707400	Enhancers	Stomach Mucosa	stomach

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