Variant report

Variant	rs6872509
Chromosome Location	chr5:59881945-59881946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:59105946..59106527-chr5:59881839..59882378,2	K562	blood:
2	chr5:59880816..59882802-chr5:59922734..59926051,3	K562	blood:
3	chr5:59880816..59882802-chr5:59924058..59926051,2	K562	blood:
4	chr5:59678290..59679528-chr5:59881870..59883189,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000035499	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1026418	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10516154	1.00[ASN][1000 genomes]
rs11957512	1.00[ASN][1000 genomes]
rs11960912	1.00[ASN][1000 genomes]
rs1379111	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1563516	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs16878190	1.00[ASN][1000 genomes]
rs16878304	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878315	1.00[CEU][hapmap]
rs1870012	1.00[CEU][hapmap]
rs1870013	1.00[CEU][hapmap]
rs2045355	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2061252	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061254	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124751	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2124753	0.82[AFR][1000 genomes]
rs2409763	1.00[ASN][1000 genomes]
rs2441051	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441052	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2591635	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606688	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286150	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286151	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286152	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286157	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286159	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857237	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887175	1.00[ASN][1000 genomes]
rs3909458	1.00[ASN][1000 genomes]
rs7702459	1.00[CEU][hapmap]
rs7706896	1.00[CEU][hapmap]
rs7708849	1.00[CEU][hapmap]
rs7712043	1.00[CEU][hapmap]
rs7719525	1.00[CEU][hapmap]
rs7728865	1.00[ASN][1000 genomes]
rs897671	1.00[CEU][hapmap]
rs9686946	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	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59873000-59908600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:59873000-59908800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:59873200-59911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:59874600-59889600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:59874600-59890400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:59875400-59895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:59875400-59895800	Weak transcription	Fetal Thymus	thymus
8	chr5:59875400-59899400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:59876400-59890600	Weak transcription	Dnd41	blood
11	chr5:59879000-59886000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:59879400-59882400	Enhancers	GM12878-XiMat	blood
13	chr5:59881200-59882000	Enhancers	Primary B cells from peripheral blood	blood
14	chr5:59881200-59882200	Enhancers	Stomach Mucosa	stomach
15	chr5:59881400-59882200	Enhancers	Primary B cells from cord blood	blood
16	chr5:59881600-59882200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr5:59881600-59882400	Enhancers	Pancreatic Islets	Pancreatic Islet

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