Variant report

Variant	rs6561638
Chromosome Location	chr13:52095838-52095839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52093545..52096468-chr13:52097107..52099629,3	MCF-7	breast:
2	chr13:52088586..52090282-chr13:52095773..52098356,2	MCF-7	breast:
3	chr13:52025069..52031067-chr13:52092672..52100320,19	MCF-7	breast:
4	chr13:52021229..52031054-chr13:52088479..52100505,23	MCF-7	breast:
5	chr13:52093719..52095925-chr13:52134002..52136713,2	MCF-7	breast:
6	chr13:52026880..52029766-chr13:52094473..52098011,4	K562	blood:
7	chr13:52093115..52097623-chr13:52157437..52160245,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224892	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs17597531	1.00[ASW][hapmap]
rs2277443	1.00[ASW][hapmap]
rs2483425	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2764603	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3908968	1.00[ASW][hapmap]
rs4555048	1.00[ASW][hapmap]
rs4643202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6561640	0.91[ASN][1000 genomes]
rs7336177	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526775	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526786	1.00[ASW][hapmap]
rs9526788	1.00[ASW][hapmap]
rs9535652	1.00[ASW][hapmap]
rs9535656	1.00[MKK][hapmap]
rs9535661	1.00[ASW][hapmap]
rs9535663	1.00[ASW][hapmap]
rs9535665	1.00[ASW][hapmap]
rs9535699	1.00[ASW][hapmap]
rs9535717	1.00[ASW][hapmap];0.85[GIH][hapmap]
rs9535722	1.00[ASW][hapmap];0.85[GIH][hapmap]
rs9535739	1.00[ASW][hapmap]
rs9563046	1.00[ASW][hapmap]
rs9568618	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6561638	WDFY2	cis	cerebellum	SCAN
rs6561638	INTS6	Cis_1M	lymphoblastoid	RTeQTL
rs6561638	HNRNPA1L2	cis	cerebellum	SCAN
rs6561638	CKAP2	cis	parietal	SCAN
rs6561638	WDFY2	cis	multi-tissue	Pritchard
rs6561638	PTPRB	trans	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52090000-52097400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:52093200-52097000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr13:52093200-52097200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr13:52093400-52096000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr13:52093400-52096200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr13:52093400-52097000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr13:52093400-52097000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr13:52093400-52097000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr13:52093400-52097200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr13:52093800-52097000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr13:52093800-52097800	Enhancers	HepG2	liver
12	chr13:52094200-52097200	Weak transcription	NHLF	lung
13	chr13:52094600-52097200	Weak transcription	NHDF-Ad	bronchial
14	chr13:52094600-52099000	Weak transcription	HSMM	muscle
15	chr13:52094800-52097000	Weak transcription	NHEK	skin
16	chr13:52094800-52097000	Weak transcription	Osteobl	bone
17	chr13:52094800-52097200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:52094800-52097200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr13:52094800-52097200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr13:52094800-52097200	Weak transcription	Fetal Muscle Leg	muscle
21	chr13:52094800-52097400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr13:52094800-52098200	Enhancers	A549	lung
23	chr13:52094800-52098800	Weak transcription	NH-A	brain
24	chr13:52094800-52100800	Enhancers	Hela-S3	cervix
25	chr13:52095000-52096000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:52095000-52096600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr13:52095000-52097200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr13:52095000-52097200	Weak transcription	Fetal Thymus	thymus
29	chr13:52095000-52097200	Weak transcription	HMEC	breast
30	chr13:52095200-52097000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr13:52095200-52097200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:52095200-52097200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr13:52095400-52097200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr13:52095600-52097200	Weak transcription	Primary T cells from cord blood	blood
35	chr13:52095800-52096000	Enhancers	Liver	Liver
36	chr13:52095800-52096200	ZNF genes & repeats	Aorta	Aorta

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