Variant report

Variant	rs12516014
Chromosome Location	chr5:97742830-97742831
allele	A/C
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	CTCF	chr5:97742740-97742890	HMEC	breast:	n/a	chr5:97742741-97742750
2	CTCF	chr5:97742680-97742830	NHEK	skin:	n/a	chr5:97742741-97742750
3	CTCF	chr5:97742680-97742830	MCF-7	breast:	n/a	chr5:97742741-97742750
4	CTCF	chr5:97742800-97742950	GM12875	blood:	n/a	n/a
5	CTCF	chr5:97742760-97742910	BE2_C	brain:	n/a	n/a
6	CTCF	chr5:97742700-97742850	GM12872	blood:	n/a	chr5:97742741-97742750
7	CTCF	chr5:97742680-97742830	HPAF	blood vessel:	n/a	chr5:97742741-97742750
8	CTCF	chr5:97742700-97742850	NB4	blood:	n/a	chr5:97742741-97742750
9	CTCF	chr5:97742680-97742830	HEEpiC	esophagus:	n/a	chr5:97742741-97742750
10	CTCF	chr5:97742581-97742934	GM12878	blood:	n/a	chr5:97742741-97742750
11	RAD21	chr5:97742520-97742879	MCF-7	breast:	n/a	n/a
12	CTCF	chr5:97742680-97742830	HEK293	kidney:	n/a	chr5:97742741-97742750
13	CTCF	chr5:97742680-97742830	Caco-2	colon:	n/a	chr5:97742741-97742750
14	CTCF	chr5:97742720-97742870	GM12864	blood:	n/a	chr5:97742741-97742750
15	RAD21	chr5:97742494-97742897	SK-N-SH_RA	brain:	n/a	n/a
16	CTCF	chr5:97742680-97742830	HVMF	connective:	n/a	chr5:97742741-97742750
17	CTCF	chr5:97742680-97742830	GM12866	blood:	n/a	chr5:97742741-97742750
18	CTCF	chr5:97742680-97742830	GM12873	blood:	n/a	chr5:97742741-97742750
19	CTCF	chr5:97742659-97742859	IMR90	lung:	n/a	chr5:97742741-97742750
20	CTCF	chr5:97742720-97742870	HCT-116	colon:	n/a	chr5:97742741-97742750
21	RAD21	chr5:97742520-97743009	MCF-7	breast:	n/a	n/a
22	CTCF	chr5:97742740-97742890	HFF-Myc	foreskin:	n/a	chr5:97742741-97742750
23	CTCF	chr5:97742515-97742882	MCF-7	breast:	n/a	chr5:97742741-97742750
24	CTCF	chr5:97742720-97742870	HFF	foreskin:	n/a	chr5:97742741-97742750
25	CTCF	chr5:97742700-97742850	SK-N-SH_RA	brain:	n/a	chr5:97742741-97742750
26	RAD21	chr5:97742536-97742837	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
MRPS35P2	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10035546	1.00[ASN][1000 genomes]
rs10036788	0.89[ASN][1000 genomes]
rs10036839	0.89[ASN][1000 genomes]
rs10050404	1.00[CEU][hapmap]
rs10050543	1.00[ASN][1000 genomes]
rs10054643	0.89[ASN][1000 genomes]
rs10076590	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11950953	0.89[ASN][1000 genomes]
rs11953877	0.89[ASN][1000 genomes]
rs11953894	0.89[ASN][1000 genomes]
rs11954911	0.89[ASN][1000 genomes]
rs11955115	0.89[ASN][1000 genomes]
rs11959995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516667	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517476	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519087	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12520566	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523434	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1455424	0.89[ASN][1000 genomes]
rs1455425	0.89[ASN][1000 genomes]
rs1455426	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1455432	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17165943	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35382921	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4702968	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4702970	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703066	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703070	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4703347	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703354	1.00[ASN][1000 genomes]
rs59277777	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59423561	0.89[ASN][1000 genomes]
rs60249733	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62369875	0.89[ASN][1000 genomes]
rs6594645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594647	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6596727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap]
rs6596748	0.89[ASN][1000 genomes]
rs6862206	0.89[ASN][1000 genomes]
rs6863762	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6870895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872831	0.89[ASN][1000 genomes]
rs6877032	0.89[ASN][1000 genomes]
rs6885408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890493	1.00[ASN][1000 genomes]
rs73143833	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159220	0.89[ASN][1000 genomes]
rs73159222	0.89[ASN][1000 genomes]
rs73159223	0.89[ASN][1000 genomes]
rs73159226	0.89[ASN][1000 genomes]
rs73159258	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702659	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702702	1.00[ASN][1000 genomes]
rs7714842	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734263	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734271	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882407	chr5:97553255-97783046	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv882408	chr5:97616089-97836794	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv830419	chr5:97653713-97829079	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1018555	chr5:97719032-97873906	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:97740400-97744200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links