Variant report

Variant	rs968350
Chromosome Location	chr14:38070974-38070975
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	POLR2A	chr14:38070513-38071402	HepG2	liver:	n/a	n/a
2	POLR2A	chr14:38069873-38071168	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:38065477..38068089-chr14:38070439..38072783,2	K562	blood:
2	chr14:37722315..37724544-chr14:38070398..38072993,2	MCF-7	breast:

Variant related genes	Relation type
FOXA1	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1008236	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10133438	0.86[CHB][hapmap]
rs10143976	0.87[CHD][hapmap]
rs10144334	0.82[ASN][1000 genomes]
rs10145379	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10145473	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs10149161	0.82[EUR][1000 genomes]
rs10151200	0.86[CHB][hapmap]
rs10400689	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap]
rs1057536	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11156961	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs11156962	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs1155456	0.87[CHD][hapmap]
rs1158701	0.86[CHB][hapmap]
rs1159151	0.86[CHB][hapmap]
rs11623989	0.83[CHD][hapmap]
rs11627807	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11627844	0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1169873	0.86[CHD][hapmap]
rs11846416	0.82[ASN][1000 genomes]
rs1547009	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs1814005	0.87[CHD][hapmap]
rs1884798	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1884803	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs1950824	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs1950826	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs1955934	0.83[CHD][hapmap]
rs1956427	0.87[CHD][hapmap]
rs1956429	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1956433	0.87[CHD][hapmap]
rs1956437	0.87[CHD][hapmap]
rs1956442	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs1956443	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs1980675	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs2146133	0.87[CHD][hapmap]
rs2180609	0.87[CHD][hapmap]
rs2415404	0.87[CHD][hapmap]
rs4900918	0.87[CHD][hapmap]
rs4900945	0.87[CHD][hapmap]
rs4900969	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs4901012	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6571814	0.87[CHD][hapmap]
rs7144658	0.83[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7146299	0.87[CHD][hapmap]
rs7146958	0.82[ASN][1000 genomes]
rs7147379	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153426	0.87[CHD][hapmap]
rs7153867	0.82[ASN][1000 genomes]
rs7159456	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs7160774	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7161228	0.89[ASN][1000 genomes]
rs7161326	0.86[CHD][hapmap]
rs7493775	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs762083	0.94[ASN][1000 genomes]
rs8005136	0.83[CHD][hapmap]
rs8016138	0.83[ASN][1000 genomes]
rs8019713	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs996916	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530038	chr14:37590543-38336191	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv826923	chr14:38017619-38108645	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv832772	chr14:38030300-38225921	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	nsv901642	chr14:38041870-38081005	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv901643	chr14:38047789-38081005	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
6	nsv901646	chr14:38051035-38081005	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv916985	chr14:38052347-38838551	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs968350	SEC23A	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38069400-38071000	Enhancers	Liver	Liver
2	chr14:38069400-38071800	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr14:38069600-38071000	Weak transcription	Pancreas	Pancrea
4	chr14:38069600-38071000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
5	chr14:38069600-38071800	Weak transcription	Gastric	stomach
6	chr14:38069800-38071000	Bivalent Enhancer	Fetal Intestine Large	intestine
7	chr14:38069800-38071200	Bivalent Enhancer	Fetal Intestine Small	intestine
8	chr14:38069800-38071800	Enhancers	HepG2	liver
9	chr14:38070200-38071200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
10	chr14:38070400-38071800	Weak transcription	A549	lung
11	chr14:38070800-38071000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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