Variant report

Variant	rs10845563
Chromosome Location	chr12:12659894-12659895
allele	A/G
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	EP300	chr12:12658292-12660593	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr12:12658327-12660010	SK-N-SH	brain:	n/a	chr12:12659276-12659283 chr12:12659276-12659285 chr12:12659276-12659283 chr12:12659274-12659286 chr12:12659275-12659285 chr12:12659276-12659283 chr12:12659277-12659294 chr12:12659272-12659288 chr12:12659387-12659403 chr12:12659276-12659285
3	TCF12	chr12:12658487-12660034	SK-N-SH	brain:	n/a	chr12:12659784-12659793
4	GATA3	chr12:12658514-12659952	SK-N-SH	brain:	n/a	chr12:12659276-12659283 chr12:12659276-12659285 chr12:12659276-12659283 chr12:12659274-12659286 chr12:12659275-12659285 chr12:12659276-12659283 chr12:12659277-12659294 chr12:12659272-12659288 chr12:12659387-12659403 chr12:12659276-12659285
5	POLR2A	chr12:12658738-12659923	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr12:12659776-12659941	ProgFib	skin:	n/a	n/a
7	POLR2A	chr12:12658773-12660365	PFSK-1	brain:	n/a	n/a
8	MXI1	chr12:12658198-12660039	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr12:12659514-12659945	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12659166..12661033-chr12:12690816..12693581,2	MCF-7	breast:

Variant related genes	Relation type
DUSP16	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10743988	0.81[AFR][1000 genomes]
rs10743989	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845552	0.80[MEX][hapmap]
rs10845554	0.84[CEU][hapmap]
rs10845559	0.81[CEU][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap]
rs10845560	0.81[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap]
rs10845562	0.92[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs10845567	0.80[AFR][1000 genomes]
rs11054937	0.81[AFR][1000 genomes]
rs11054940	0.81[GIH][hapmap]
rs11054941	0.81[CEU][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes]
rs11054942	0.81[GIH][hapmap]
rs12424448	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs12819116	0.92[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs17312926	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs17379216	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs2287206	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2417189	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2417191	0.92[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs4255620	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs744170	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs747726	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7972902	0.81[GIH][hapmap]
rs933575	0.89[GIH][hapmap];0.80[MEX][hapmap]
rs962928	0.81[CEU][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap]

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	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
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10845563	AICDA	cis	cerebellum	SCAN
rs10845563	CLEC2B	cis	cerebellum	SCAN
rs10845563	ETV6	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12630600-12661200	Weak transcription	NHEK	skin
2	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
3	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
4	chr12:12639400-12679600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:12641600-12663600	Weak transcription	Lung	lung
6	chr12:12641600-12686200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:12647000-12661400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:12652800-12665000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:12653800-12669000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:12654000-12661200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:12654200-12660400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:12654400-12667200	Weak transcription	Primary T cells from cord blood	blood
13	chr12:12656000-12666400	Weak transcription	Spleen	Spleen
14	chr12:12656600-12660600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:12656800-12670800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:12657400-12660400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:12657600-12660400	Enhancers	Fetal Intestine Large	intestine
18	chr12:12658000-12660400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:12658000-12660800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:12658000-12660800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:12658200-12660000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:12658200-12660000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:12658200-12660400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:12658200-12660400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:12658200-12660400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr12:12658200-12660400	Enhancers	Placenta	Placenta
27	chr12:12658200-12660400	Enhancers	Fetal Stomach	stomach
28	chr12:12658200-12660400	Enhancers	Right Ventricle	heart
29	chr12:12658200-12660400	Enhancers	Small Intestine	intestine
30	chr12:12658200-12660600	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr12:12658200-12660800	Enhancers	Pancreas	Pancrea
32	chr12:12658200-12661800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr12:12658200-12662800	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr12:12658400-12660000	Flanking Active TSS	NHDF-Ad	bronchial
35	chr12:12658400-12660400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:12658400-12660400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr12:12658400-12660400	Enhancers	NH-A	brain
38	chr12:12658400-12662000	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr12:12658400-12662600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr12:12658400-12662800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr12:12658600-12660400	Enhancers	H9 Cell Line	embryonic stem cell
42	chr12:12658800-12660400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:12658800-12660400	Enhancers	HSMMtube	muscle
44	chr12:12658800-12662200	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr12:12658800-12662600	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr12:12659000-12660000	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr12:12659000-12660400	Active TSS	Aorta	Aorta
48	chr12:12659000-12662800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:12659000-12667000	Weak transcription	Fetal Thymus	thymus
50	chr12:12659000-12669200	Weak transcription	Primary T cells fromperipheralblood	blood

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