Variant report

Variant	rs933575
Chromosome Location	chr12:12636234-12636235
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	MTA3	chr12:12635336-12636302	GM12878	blood:	n/a	n/a
2	RUNX3	chr12:12635768-12636306	GM12878	blood:	n/a	n/a
3	SPI1	chr12:12635942-12636307	HL-60	blood:	n/a	chr12:12636145-12636158 chr12:12636199-12636212
4	NFATC1	chr12:12635410-12636236	GM12878	blood:	n/a	n/a
5	EP300	chr12:12635838-12636251	GM12878	blood:	n/a	chr12:12636148-12636157
6	CHD2	chr12:12635845-12636243	GM12878	blood:	n/a	n/a
7	CUX1	chr12:12635953-12636531	GM12878	blood:	n/a	n/a
8	RUNX3	chr12:12635837-12636234	GM12878	blood:	n/a	n/a
9	TBP	chr12:12636094-12636475	GM12878	blood:	n/a	n/a
10	EP300	chr12:12635918-12636332	GM12878	blood:	n/a	chr12:12636148-12636157
11	NFIC	chr12:12635763-12636388	GM12878	blood:	n/a	n/a
12	EP300	chr12:12635936-12636338	GM12878	blood:	n/a	chr12:12636148-12636157

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12634486..12639853-chr12:12714024..12717789,5	K562	blood:
2	chr12:12634008..12636431-chr12:12645657..12647328,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255670	TF binding region
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10743988	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772570	0.81[ASN][1000 genomes]
rs10845552	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10845556	0.84[EUR][1000 genomes]
rs10845559	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845560	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845563	0.89[GIH][hapmap];0.80[MEX][hapmap]
rs10845567	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845572	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs11054937	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054940	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs11054941	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054942	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs11054947	0.91[ASN][1000 genomes]
rs11613385	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs12422540	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1558822	0.93[ASN][1000 genomes]
rs2111271	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2287206	1.00[ASW][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2417190	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs3815591	0.88[ASN][1000 genomes]
rs4255620	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763832	0.85[ASN][1000 genomes]
rs4763833	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs7137455	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs7294378	0.92[ASN][1000 genomes]
rs7295305	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs7295427	0.88[ASN][1000 genomes]
rs7310652	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972902	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[ASN][1000 genomes]
rs962927	0.88[CEU][hapmap];0.82[MKK][hapmap]
rs962928	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs933575	LOH12CR1	cis	lymphoblastoid	seeQTL
rs933575	ETV6	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12603800-12639200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:12610800-12658000	Weak transcription	NHDF-Ad	bronchial
3	chr12:12618400-12642200	Weak transcription	Stomach Mucosa	stomach
4	chr12:12621400-12645400	Weak transcription	Small Intestine	intestine
5	chr12:12621600-12646000	Weak transcription	Psoas Muscle	Psoas
6	chr12:12621600-12646200	Weak transcription	Brain Germinal Matrix	brain
7	chr12:12622600-12653800	Weak transcription	Fetal Heart	heart
8	chr12:12624000-12638000	Weak transcription	HMEC	breast
9	chr12:12626400-12639000	Strong transcription	Placenta	Placenta
10	chr12:12626600-12636600	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:12626600-12636800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:12626600-12639200	Strong transcription	Liver	Liver
13	chr12:12626800-12640400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:12626800-12653600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:12627200-12636800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:12627400-12636600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:12627400-12639200	Strong transcription	HepG2	liver
18	chr12:12627400-12640000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:12627600-12636800	Strong transcription	Adipose Nuclei	Adipose
20	chr12:12627600-12637200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr12:12627600-12640200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:12627600-12642400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:12627800-12636800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:12627800-12646200	Weak transcription	Fetal Brain Male	brain
25	chr12:12628400-12636800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr12:12628400-12639800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:12628600-12647600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr12:12628800-12636600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:12628800-12655800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:12629400-12636600	Strong transcription	Left Ventricle	heart
31	chr12:12630600-12641200	Weak transcription	HSMM	muscle
32	chr12:12630600-12661200	Weak transcription	NHEK	skin
33	chr12:12630800-12636400	Weak transcription	Spleen	Spleen
34	chr12:12630800-12637800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:12630800-12639000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:12630800-12639200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr12:12630800-12640000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:12630800-12640800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr12:12630800-12640800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:12630800-12641400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:12630800-12655800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:12630800-12658200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:12630800-12658400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr12:12630800-12659600	Weak transcription	Esophagus	oesophagus
45	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
46	chr12:12631000-12636800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:12631000-12645200	Weak transcription	Gastric	stomach
48	chr12:12631400-12641000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:12631800-12639000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:12632000-12637800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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