Variant report

Variant	rs883404
Chromosome Location	chr12:32584446-32584447
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32580165..32582932-chr12:32583223..32584880,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10771944	0.82[AMR][1000 genomes]
rs10844194	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs10844202	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051966	1.00[CEU][hapmap];0.86[MEX][hapmap];0.91[AMR][1000 genomes]
rs11051967	0.85[CEU][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs11051980	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11051993	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11052006	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367135	0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12815894	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12819555	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1566513	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2047643	0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs2087166	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2388991	0.80[CHB][hapmap]
rs61927215	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488053	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7299524	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312869	0.88[EUR][1000 genomes]
rs7971525	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
3	nsv469346	chr12:32531220-32587465	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv558188	chr12:32531220-32587465	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv469347	chr12:32555846-32602079	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv558189	chr12:32555846-32602079	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs883404	OVCH1	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32554600-32593200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:32573400-32587000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:32573400-32593400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:32574800-32587200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:32576200-32588800	Weak transcription	NHEK	skin
6	chr12:32576200-32589000	Weak transcription	HMEC	breast
7	chr12:32576200-32589200	Weak transcription	Stomach Mucosa	stomach
8	chr12:32580400-32593200	Weak transcription	Fetal Intestine Large	intestine
9	chr12:32582200-32587400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:32582600-32587000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:32582600-32589200	Weak transcription	Ovary	ovary
12	chr12:32582600-32589400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:32582600-32591000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:32582600-32593600	Weak transcription	Fetal Stomach	stomach
15	chr12:32582600-32598600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:32582800-32587200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:32582800-32590200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:32582800-32590400	Weak transcription	Fetal Intestine Small	intestine
19	chr12:32583000-32588200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:32583000-32588800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:32583200-32585000	Enhancers	HUVEC	blood vessel
22	chr12:32583200-32588800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:32584000-32587000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:32584000-32587400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:32584000-32589000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:32584200-32584600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:32584200-32587400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:32584200-32587400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:32584200-32588400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:32584200-32591200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:32584400-32588600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links