Variant report

Variant	rs13419437
Chromosome Location	chr2:178774704-178774705
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	FOS	chr2:178774631-178775108	MCF10A-Er-Src	breast:	n/a	chr2:178774846-178774854 chr2:178774845-178774855 chr2:178774846-178774853
2	POLR2A	chr2:178774537-178775075	H1-neurons	neurons:	n/a	n/a
3	FOS	chr2:178774614-178775429	MCF10A-Er-Src	breast:	n/a	chr2:178774846-178774854 chr2:178775303-178775313 chr2:178775401-178775413 chr2:178775303-178775313 chr2:178774845-178774855 chr2:178774846-178774853 chr2:178775313-178775322
4	FOS	chr2:178774630-178775474	MCF10A-Er-Src	breast:	n/a	chr2:178774846-178774854 chr2:178775303-178775313 chr2:178775401-178775413 chr2:178775303-178775313 chr2:178774845-178774855 chr2:178774846-178774853 chr2:178775313-178775322
5	FOS	chr2:178774670-178775476	MCF10A-Er-Src	breast:	n/a	chr2:178774846-178774854 chr2:178775303-178775313 chr2:178775401-178775413 chr2:178775303-178775313 chr2:178774845-178774855 chr2:178774846-178774853 chr2:178775313-178775322
6	POLR2A	chr2:178774562-178775158	H1-neurons	neurons:	n/a	n/a
7	MYC	chr2:178774630-178775095	MCF10A-Er-Src	breast:	n/a	chr2:178774845-178774854 chr2:178774846-178774855
8	MYC	chr2:178774674-178775138	MCF10A-Er-Src	breast:	n/a	chr2:178774845-178774854 chr2:178774846-178774855
9	JUND	chr2:178774697-178775039	HepG2	liver:	n/a	chr2:178774846-178774854 chr2:178774844-178774855 chr2:178774845-178774855 chr2:178774846-178774853

No.	Distal block	Cell Line	Cell type
1	chr2:178770676..178772578-chr2:178773100..178774793,2	MCF-7	breast:
2	chr2:178768646..178770687-chr2:178773166..178775066,2	K562	blood:
3	chr2:178773541..178777699-chr2:178778519..178781907,4	K562	blood:

Variant related genes	Relation type
PDE11A	TF binding region
ENSG00000128655	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10164920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10165089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10168605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10171247	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs10171486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10174066	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10174604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180052	1.00[CEU][hapmap]
rs10181377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182833	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189134	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs10190066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10190805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10191328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10192990	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10195497	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197020	1.00[CEU][hapmap]
rs10197329	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs10198681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200643	1.00[CEU][hapmap]
rs10202989	1.00[CEU][hapmap]
rs10207459	1.00[CEU][hapmap]
rs10208501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10211057	1.00[CEU][hapmap]
rs10211341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10221783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10221806	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs10497477	1.00[CEU][hapmap]
rs10497478	1.00[CEU][hapmap]
rs10497481	1.00[CEU][hapmap]
rs10497483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930819	1.00[CEU][hapmap]
rs12151755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693123	0.86[AFR][1000 genomes]
rs12693127	0.87[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs12693128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693145	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693147	1.00[CEU][hapmap]
rs12988331	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990471	0.87[CEU][hapmap]
rs12994913	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12995449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13003683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13008170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13008780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13009350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13010993	0.89[AFR][1000 genomes]
rs13015148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017026	1.00[CEU][hapmap]
rs13021204	1.00[CEU][hapmap]
rs13023049	1.00[CEU][hapmap]
rs13026481	1.00[CEU][hapmap]
rs13027582	1.00[CEU][hapmap]
rs13028692	1.00[CEU][hapmap]
rs13386418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13386639	1.00[CEU][hapmap]
rs13388218	0.97[AFR][1000 genomes]
rs13389574	1.00[CEU][hapmap]
rs13392577	1.00[CEU][hapmap]
rs13393722	0.87[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs13396207	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13400109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13400411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13402629	1.00[CEU][hapmap]
rs13402636	1.00[CEU][hapmap]
rs13405585	1.00[CEU][hapmap]
rs13410185	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410486	1.00[CEU][hapmap]
rs13411527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13411542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13411922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13411970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13413095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13413731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13422276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13422706	1.00[CEU][hapmap]
rs13425873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13426862	1.00[CEU][hapmap]
rs13427912	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429445	1.00[CEU][hapmap]
rs1358299	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1527291	1.00[JPT][hapmap]
rs16865821	1.00[JPT][hapmap]
rs16865846	1.00[JPT][hapmap]
rs17329742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17329956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17329998	1.00[CEU][hapmap]
rs17330012	1.00[CEU][hapmap]
rs17330172	1.00[CEU][hapmap]
rs17330290	1.00[CEU][hapmap]
rs17330381	1.00[CEU][hapmap]
rs17401293	1.00[CEU][hapmap]
rs17401468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17401650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17401671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17401860	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17401902	1.00[CEU][hapmap]
rs17401916	1.00[CEU][hapmap]
rs17401951	1.00[CEU][hapmap]
rs17402102	1.00[CEU][hapmap]
rs17635803	1.00[CEU][hapmap]
rs17635875	1.00[CEU][hapmap]
rs17635957	1.00[CEU][hapmap]
rs17687170	1.00[CEU][hapmap]
rs17687217	1.00[CEU][hapmap]
rs1898012	1.00[JPT][hapmap]
rs2043548	1.00[CEU][hapmap]
rs34596457	0.81[AFR][1000 genomes]
rs35267683	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35385829	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35625771	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35758079	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3861373	1.00[CEU][hapmap]
rs4377360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4423634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6708449	1.00[JPT][hapmap]
rs6726477	1.00[CEU][hapmap]
rs6738614	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs6750238	1.00[JPT][hapmap]
rs71423515	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423518	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423519	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575322	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs7600368	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9288011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989802	0.97[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533377	chr2:178718801-178963463	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1007579	chr2:178729330-178890946	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875451	chr2:178748294-178953409	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv998304	chr2:178756380-178924378	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv536056	chr2:178756380-178924378	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178768600-178780000	Weak transcription	Psoas Muscle	Psoas
2	chr2:178773400-178774800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:178773800-178774800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:178774000-178775000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:178774200-178774800	Enhancers	Fetal Kidney	kidney
6	chr2:178774200-178775800	Enhancers	HMEC	breast
7	chr2:178774200-178776000	Enhancers	NHEK	skin
8	chr2:178774400-178774800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:178774600-178774800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:178774600-178775600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:178774600-178775800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:178774600-178776000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links