Variant report

Variant	rs1183910
Chromosome Location	chr12:121420807-121420808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr12:121420476-121420825	K562	blood:	n/a	n/a
2	POLR2A	chr12:121420408-121421289	HepG2	liver:	n/a	n/a
3	RCOR1	chr12:121420407-121420979	K562	blood:	n/a	n/a
4	TCF12	chr12:121420052-121420919	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121419406..121422092-chr12:121422475..121425429,2	K562	blood:
2	chr12:121412159..121414001-chr12:121420552..121422609,2	MCF-7	breast:
3	chr12:121419295..121421296-chr12:121428164..121430442,2	MCF-7	breast:
4	chr12:120803152..120806050-chr12:121419474..121422270,2	K562	blood:
5	chr12:121416581..121418752-chr12:121419164..121421756,2	K562	blood:

No data

Variant related genes	Relation type
HNF1A-AS1	TF binding region
ENSG00000135097	Chromatin interaction
ENSG00000241388	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11065384	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11065385	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1169284	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169286	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs1169288	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1169289	0.87[ASN][1000 genomes]
rs1169292	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1169294	0.95[EUR][1000 genomes]
rs1169300	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs1169306	0.91[YRI][hapmap]
rs1169310	0.91[YRI][hapmap]
rs1169312	0.91[YRI][hapmap]
rs1169313	0.91[YRI][hapmap]
rs1169314	0.85[JPT][hapmap];0.89[YRI][hapmap]
rs1732391	0.84[AMR][1000 genomes]
rs2243458	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2244608	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2251468	0.86[AMR][1000 genomes]
rs2257764	0.90[YRI][hapmap]
rs2259816	0.91[YRI][hapmap]
rs2264750	0.84[AFR][1000 genomes]
rs2393775	0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2393776	0.94[ASN][1000 genomes]
rs2393791	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2464195	0.91[YRI][hapmap]
rs2464196	0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs2650000	0.84[AMR][1000 genomes]
rs6489786	0.85[AMR][1000 genomes]
rs7310409	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs735396	0.91[YRI][hapmap]
rs7954039	0.84[AMR][1000 genomes]
rs7954331	0.84[AMR][1000 genomes]
rs7970695	0.96[ASN][1000 genomes]
rs7979473	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7979478	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9738226	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	esv3357747	chr12:121405281-121427388	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1037195	chr12:121408540-121470375	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

Variant related diseases (count:3)

Disease	PMID	Source
C-reactive protein	19567438	GWAS catalog
C-reactive protein levels	21300955	GWAS catalog
C-reactive protein	23844046	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121409600-121422200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:121418200-121421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:121418600-121421000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:121418600-121422000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:121418600-121422200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:121418600-121441000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:121418800-121421600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:121418800-121422200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:121418800-121422200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:121418800-121422200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:121418800-121431800	Weak transcription	Fetal Stomach	stomach
12	chr12:121418800-121439400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:121419000-121421200	Enhancers	Gastric	stomach
14	chr12:121419000-121422000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:121419200-121421200	Enhancers	Pancreas	Pancrea
16	chr12:121419200-121431600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:121419400-121421800	Enhancers	Liver	Liver
18	chr12:121419400-121422200	Weak transcription	Fetal Lung	lung
19	chr12:121419400-121422200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr12:121419400-121423400	Enhancers	Stomach Mucosa	stomach
21	chr12:121419600-121421000	Genic enhancers	HepG2	liver
22	chr12:121419600-121421800	Weak transcription	Fetal Kidney	kidney
23	chr12:121419600-121422000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:121419600-121424200	Genic enhancers	Fetal Intestine Small	intestine
25	chr12:121419600-121441000	Weak transcription	Small Intestine	intestine
26	chr12:121419800-121421600	Genic enhancers	Fetal Intestine Large	intestine
27	chr12:121419800-121421600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:121419800-121422000	Weak transcription	Colonic Mucosa	Colon
29	chr12:121419800-121429800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:121420000-121421800	Enhancers	A549	lung
31	chr12:121420600-121421200	Genic enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links