Variant report

Variant	rs13189446
Chromosome Location	chr5:61572989-61572990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61570576..61576152-chr5:61577980..61582631,7	K562	blood:
2	chr5:61570852..61575397-chr5:61600002..61603728,9	K562	blood:
3	chr5:61570852..61575074-chr5:61600002..61604457,10	K562	blood:
4	chr5:61571856..61574619-chr5:61696505..61699367,2	K562	blood:
5	chr5:61571147..61572996-chr5:61698680..61700895,2	K562	blood:

Variant related genes	Relation type
ENSG00000086189	Chromatin interaction
ENSG00000068796	Chromatin interaction
ENSG00000086200	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1108158	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740652	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11742167	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11747516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11750109	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12655562	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13155253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13156073	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13156695	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13161789	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13162519	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13162821	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13169321	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13170425	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13174779	0.89[ASN][1000 genomes]
rs13176923	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13178729	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13181377	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs153860	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs153864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs153866	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs153869	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs153873	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs16875037	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890628	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890651	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16898838	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17382217	1.00[CEU][hapmap]
rs2059162	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2063255	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272291	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2441115	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs27090	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs34220654	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34596001	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35011	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs35012	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs35058	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs35238667	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35311093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35572300	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35672643	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35699711	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35744020	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35746052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35794032	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35808056	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35815430	0.83[EUR][1000 genomes]
rs35842742	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36105063	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776612	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776614	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3822487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4289514	0.89[ASN][1000 genomes]
rs71617425	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71617426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71617427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71617428	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7446543	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs814169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs971965	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv830318	chr5:61415713-61623320	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv2755585	chr5:61535831-61618595	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv881726	chr5:61556730-61676911	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv598326	chr5:61569169-61576324	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv996027	chr5:61569356-61577045	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13189446	ARC	trans	brain	seeQTL
rs13189446	EGR4	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61571000-61574400	Enhancers	Primary hematopoietic stem cells	blood
2	chr5:61571600-61577400	Weak transcription	Fetal Intestine Small	intestine
3	chr5:61572400-61573200	Enhancers	Fetal Intestine Large	intestine
4	chr5:61572400-61573400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:61572400-61573600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:61572400-61573600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:61572400-61573600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:61572400-61574800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr5:61572600-61573000	Enhancers	HSMM	muscle
10	chr5:61572600-61573000	Active TSS	K562	blood
11	chr5:61572600-61573400	Flanking Active TSS	GM12878-XiMat	blood
12	chr5:61572600-61573600	Enhancers	A549	lung
13	chr5:61572600-61573800	Enhancers	HMEC	breast
14	chr5:61572600-61573800	Enhancers	NHEK	skin
15	chr5:61572800-61573000	Enhancers	HUVEC	blood vessel
16	chr5:61572800-61573200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr5:61572800-61573200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:61572800-61573200	Enhancers	Fetal Heart	heart
19	chr5:61572800-61573200	Enhancers	Hela-S3	cervix
20	chr5:61572800-61573400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:61572800-61573400	Enhancers	Primary T cells from cord blood	blood
22	chr5:61572800-61573400	Enhancers	Fetal Kidney	kidney
23	chr5:61572800-61573400	Enhancers	NH-A	brain

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