Variant report

Variant	rs11174404
Chromosome Location	chr12:62658720-62658721
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	CUX1	chr12:62658238-62658946	GM12878	blood:	n/a	n/a
2	IRF1	chr12:62658015-62658924	K562	blood:	n/a	chr12:62658693-62658707 chr12:62658695-62658706 chr12:62658692-62658706 chr12:62658410-62658420 chr12:62658694-62658708 chr12:62658696-62658710 chr12:62658692-62658712
3	JUN	chr12:62658635-62658791	K562	blood:	n/a	n/a
4	STAT2	chr12:62658485-62658879	K562	blood:	n/a	chr12:62658561-62658569 chr12:62658692-62658707 chr12:62658694-62658705
5	TBP	chr12:62658156-62659072	GM12878	blood:	n/a	n/a
6	IRF1	chr12:62657524-62659433	K562	blood:	n/a	chr12:62658693-62658707 chr12:62658695-62658706 chr12:62658692-62658706 chr12:62658410-62658420 chr12:62658694-62658708 chr12:62658696-62658710 chr12:62658692-62658712
7	EP300	chr12:62658640-62658942	GM12878	blood:	n/a	n/a
8	SPI1	chr12:62658600-62658848	GM12891	blood:	n/a	chr12:62658694-62658703
9	EBF1	chr12:62658676-62658876	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:62656909..62660165-chr12:62669931..62675800,5	K562	blood:
2	chr12:62655605..62659464-chr12:62666404..62669367,3	MCF-7	breast:
3	chr12:62657511..62660316-chr12:62711919..62713986,2	K562	blood:
4	chr12:62636676..62638829-chr12:62658286..62659994,2	MCF-7	breast:
5	chr12:62652133..62655871-chr12:62655983..62662487,11	MCF-7	breast:

Variant related genes	Relation type
FAM19A2	TF binding region
ENSG00000198673	Chromatin interaction
ENSG00000135655	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10431509	0.81[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10431510	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10431565	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10459253	0.83[ASN][1000 genomes]
rs10506440	0.84[ASN][1000 genomes]
rs10747958	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784292	0.81[ASN][1000 genomes]
rs10877819	0.82[CHB][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs10877820	0.87[ASN][1000 genomes]
rs10877824	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877826	0.84[ASN][1000 genomes]
rs10877829	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877831	0.96[CEU][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11174401	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174408	0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174409	0.87[ASN][1000 genomes]
rs11174410	0.87[ASN][1000 genomes]
rs11174411	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174412	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174416	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174417	0.88[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174418	0.87[ASN][1000 genomes]
rs11174420	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174423	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174424	0.96[CEU][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174428	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174431	0.84[ASN][1000 genomes]
rs11174433	0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11174435	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174436	0.81[ASN][1000 genomes]
rs11174437	0.81[ASN][1000 genomes]
rs11174438	0.95[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11174449	0.81[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs11504121	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11504122	0.82[ASN][1000 genomes]
rs11561463	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11830242	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11836268	0.84[ASN][1000 genomes]
rs12228015	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12229271	0.82[ASN][1000 genomes]
rs12231778	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12297474	0.84[ASN][1000 genomes]
rs12299072	0.87[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12306066	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12307900	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12310318	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12310616	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12310651	0.84[ASN][1000 genomes]
rs12311259	0.82[ASN][1000 genomes]
rs12311279	0.87[ASN][1000 genomes]
rs12315645	0.83[ASN][1000 genomes]
rs12317437	0.82[ASN][1000 genomes]
rs12318287	0.84[ASN][1000 genomes]
rs12424732	0.85[LWK][hapmap];0.93[MKK][hapmap]
rs1376342	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1496859	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1901239	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131434	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131435	0.87[ASN][1000 genomes]
rs2132651	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2242032	0.82[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs28526400	0.84[ASN][1000 genomes]
rs35634758	0.87[ASN][1000 genomes]
rs3803106	0.87[ASN][1000 genomes]
rs6581444	0.95[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67044039	0.87[ASN][1000 genomes]
rs67853252	0.87[ASN][1000 genomes]
rs7132814	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7133294	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7137068	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7295013	0.87[ASN][1000 genomes]
rs7298827	0.87[ASN][1000 genomes]
rs7300928	0.87[ASN][1000 genomes]
rs7302033	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302617	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7953967	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7965326	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974973	0.83[ASN][1000 genomes]
rs7976058	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902971	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][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	nsv1035150	chr12:62615347-62785005	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1049465	chr12:62657011-62785005	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1053403	chr12:62657011-62809413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11174404	USP15	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62654800-62660600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:62655000-62659400	Weak transcription	Esophagus	oesophagus
3	chr12:62655000-62663400	Weak transcription	Lung	lung
4	chr12:62655400-62660800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:62655400-62685600	Weak transcription	HSMM	muscle
6	chr12:62655600-62661400	Weak transcription	NH-A	brain
7	chr12:62655800-62659400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:62655800-62661200	Weak transcription	Osteobl	bone
9	chr12:62656000-62658800	Weak transcription	Brain Substantia Nigra	brain
10	chr12:62656000-62660800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:62656000-62661000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:62656000-62661200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:62656000-62661400	Weak transcription	Stomach Mucosa	stomach
14	chr12:62656000-62662000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:62656000-62663200	Weak transcription	Placenta	Placenta
16	chr12:62656000-62664800	Weak transcription	Fetal Stomach	stomach
17	chr12:62656000-62665400	Weak transcription	Brain Angular Gyrus	brain
18	chr12:62656000-62668200	Weak transcription	Right Atrium	heart
19	chr12:62656200-62659800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr12:62656200-62661000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:62656200-62661200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:62656400-62661200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:62656400-62669600	Enhancers	Liver	Liver
24	chr12:62656400-62679400	Weak transcription	Brain Anterior Caudate	brain
25	chr12:62656600-62659200	Enhancers	Duodenum Mucosa	Duodenum
26	chr12:62656600-62659200	Weak transcription	Small Intestine	intestine
27	chr12:62656600-62659400	Weak transcription	Right Ventricle	heart
28	chr12:62656600-62660800	Weak transcription	NHLF	lung
29	chr12:62656600-62661000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:62656600-62661000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:62656600-62661400	Weak transcription	HMEC	breast
32	chr12:62656600-62661400	Weak transcription	HUVEC	blood vessel
33	chr12:62656600-62662200	Weak transcription	Adipose Nuclei	Adipose
34	chr12:62656600-62663200	Weak transcription	Ovary	ovary
35	chr12:62656600-62664000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr12:62656600-62668400	Weak transcription	Fetal Brain Female	brain
37	chr12:62656600-62685600	Weak transcription	Aorta	Aorta
38	chr12:62656600-62685600	Weak transcription	Pancreas	Pancrea
39	chr12:62656800-62658800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:62656800-62659000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:62656800-62659400	Enhancers	Hela-S3	cervix
42	chr12:62656800-62675400	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:62657000-62659000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:62657000-62659600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:62657200-62658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:62657200-62658800	Weak transcription	NHEK	skin
47	chr12:62657400-62658800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr12:62657400-62659400	Weak transcription	Fetal Heart	heart
49	chr12:62657400-62661000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:62657400-62666600	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links