Variant report

Variant	rs11961538
Chromosome Location	chr6:39231013-39231014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:39195258..39199147-chr6:39228497..39232798,6	MCF-7	breast:
2	chr6:39228773..39231561-chr6:39235112..39238664,3	K562	blood:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1076734	1.00[CHD][hapmap]
rs11759627	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758870	0.81[EUR][1000 genomes]
rs2758873	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758879	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758880	0.84[EUR][1000 genomes]
rs2758886	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758896	1.00[ASN][1000 genomes]
rs2758902	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758903	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758905	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815033	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815034	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815043	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815047	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815059	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815060	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815062	0.81[EUR][1000 genomes]
rs4711589	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55804343	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55812552	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55889689	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56011317	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56300329	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852940	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11961538	GLO1	cis	cerebellum	SCAN
rs11961538	LOC221442	cis	cerebellum	SCAN
rs11961538	DAAM2	cis	parietal	SCAN
rs11961538	KCNK17	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39224400-39238400	Weak transcription	Spleen	Spleen
2	chr6:39227200-39236000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:39228400-39234600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:39229000-39231400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:39229000-39231800	Enhancers	Fetal Intestine Large	intestine
6	chr6:39230000-39235000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:39230600-39232000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr6:39230600-39234600	Weak transcription	Fetal Thymus	thymus
9	chr6:39230800-39231200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr6:39230800-39231200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:39230800-39231200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:39230800-39231800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr6:39230800-39231800	Enhancers	Liver	Liver
14	chr6:39231000-39231200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:39231000-39231200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:39231000-39231200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:39231000-39231400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr6:39231000-39231400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr6:39231000-39231400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr6:39231000-39231400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr6:39231000-39231800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr6:39231000-39231800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:39231000-39231800	Enhancers	Stomach Mucosa	stomach
24	chr6:39231000-39231800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr6:39231000-39232000	Enhancers	Primary hematopoietic stem cells	blood
26	chr6:39231000-39234200	Weak transcription	Fetal Intestine Small	intestine

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