Variant report

Variant	rs213434
Chromosome Location	chr5:118304390-118304391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118302817..118305365-chr5:118322521..118324091,2	MCF-7	breast:
2	chr5:118302138..118305564-chr5:118322264..118325147,4	K562	blood:

Variant related genes	Relation type
ENSG00000169570	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11241493	1.00[JPT][hapmap]
rs13170553	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs169917	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213435	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431601	1.00[ASN][1000 genomes]
rs2431602	1.00[ASN][1000 genomes]
rs2442123	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299191	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs299194	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs299201	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299205	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299206	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs299208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs299209	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs299214	1.00[JPT][hapmap]
rs368569	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs411110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333791	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][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	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1017548	chr5:118276479-118358394	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1015878	chr5:118288904-118414706	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537881	chr5:118288904-118414706	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv964930	chr5:118301974-118317943	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs213434	FAM170A	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118259600-118305000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr5:118263000-118306000	Weak transcription	Primary T cells from cord blood	blood
3	chr5:118296800-118314400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:118299400-118304600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:118302800-118305000	Weak transcription	Pancreas	Pancrea
6	chr5:118304000-118304400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:118304000-118304400	Enhancers	Primary B cells from peripheral blood	blood
8	chr5:118304000-118304400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:118304000-118304400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr5:118304000-118304600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr5:118304000-118304800	Weak transcription	Hela-S3	cervix
12	chr5:118304000-118305400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr5:118304000-118305400	Flanking Active TSS	HepG2	liver
14	chr5:118304200-118304400	Enhancers	Right Atrium	heart
15	chr5:118304200-118304600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr5:118304200-118304800	Weak transcription	K562	blood
17	chr5:118304200-118305000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:118304200-118305200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:118304200-118305200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:118304200-118305200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:118304200-118305200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:118304200-118305200	Enhancers	Left Ventricle	heart
23	chr5:118304200-118305400	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links