Variant report

Variant	rs12404532
Chromosome Location	chr1:220442369-220442370
allele	C/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	POLR2A	chr1:220442283-220442715	K562	blood:	n/a	n/a
2	POLR2A	chr1:220442191-220442783	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:220442272-220442610	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr1:220442127-220442632	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr1:220442308-220442683	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220440528..220443413-chr1:220443546..220445862,4	MCF-7	breast:

Variant related genes	Relation type
AURKAPS1	TF binding region
ENSG00000118873	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11095	1.00[ASW][hapmap]
rs11118508	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs12402633	0.89[EUR][1000 genomes]
rs12404566	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12409065	0.89[EUR][1000 genomes]
rs12411242	0.86[EUR][1000 genomes]
rs12568267	0.88[EUR][1000 genomes]
rs1511695	0.94[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs17563518	1.00[ASW][hapmap];0.84[MKK][hapmap]
rs17563587	1.00[ASW][hapmap];0.84[MKK][hapmap]
rs17565134	0.92[EUR][1000 genomes]
rs2048477	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738336	1.00[ASW][hapmap];0.90[JPT][hapmap];1.00[MKK][hapmap]
rs3767654	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs3814345	0.89[EUR][1000 genomes]
rs4351641	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs56074233	0.89[EUR][1000 genomes]
rs57557703	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59681037	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72747401	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72749210	0.89[EUR][1000 genomes]
rs7526460	0.89[EUR][1000 genomes]
rs7541290	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7543828	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7551804	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs866978	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[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	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12404532	MOSC2	cis	lymphoblastoid	seeQTL
rs12404532	C1orf115	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220416000-220442600	Weak transcription	Fetal Heart	heart
2	chr1:220423000-220443400	Weak transcription	Psoas Muscle	Psoas
3	chr1:220423400-220443400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:220423400-220443400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:220423800-220442600	Weak transcription	Hela-S3	cervix
6	chr1:220425200-220443400	Weak transcription	HUVEC	blood vessel
7	chr1:220426600-220443400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:220426600-220443400	Weak transcription	Right Ventricle	heart
9	chr1:220426600-220444400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:220426800-220442800	Weak transcription	Esophagus	oesophagus
11	chr1:220426800-220443400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:220426800-220443400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:220426800-220443400	Weak transcription	Ovary	ovary
14	chr1:220426800-220444000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:220426800-220444200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:220426800-220444400	Weak transcription	Colonic Mucosa	Colon
17	chr1:220426800-220445000	Weak transcription	Aorta	Aorta
18	chr1:220426800-220445000	Weak transcription	Pancreas	Pancrea
19	chr1:220427000-220442800	Weak transcription	Lung	lung
20	chr1:220427000-220443200	Weak transcription	Thymus	Thymus
21	chr1:220427000-220444200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:220427000-220445000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:220427600-220443400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:220432200-220442400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:220434800-220444800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:220435000-220443400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:220435200-220443400	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:220435800-220442800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:220436000-220443200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:220436200-220442400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:220436600-220442400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:220436800-220442600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:220437000-220443400	Strong transcription	Primary B cells from cord blood	blood
34	chr1:220437400-220442400	Weak transcription	Brain Angular Gyrus	brain
35	chr1:220437600-220443600	Weak transcription	Fetal Lung	lung
36	chr1:220437800-220443200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:220438800-220442400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr1:220438800-220442600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:220439000-220442400	Strong transcription	Primary T cells from cord blood	blood
40	chr1:220439000-220442400	Strong transcription	Fetal Thymus	thymus
41	chr1:220439000-220442600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:220439000-220442600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:220439000-220442600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:220439000-220442600	ZNF genes & repeats	GM12878-XiMat	blood
45	chr1:220439000-220443000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr1:220439000-220443200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:220439200-220442400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:220439200-220442400	Strong transcription	K562	blood
49	chr1:220439200-220443400	Weak transcription	Right Atrium	heart
50	chr1:220439400-220442400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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