Variant report

Variant	rs11616524
Chromosome Location	chr13:51548355-51548356
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	chr13:51545684..51549023-chr13:51551160..51554189,3	K562	blood:
2	chr13:51544645..51546969-chr13:51547696..51550126,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10400653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1041017	0.88[ASW][hapmap];0.85[LWK][hapmap]
rs11617366	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17075018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17075030	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56320200	0.83[ASN][1000 genomes]
rs67932352	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73186365	0.93[ASN][1000 genomes]
rs73186367	0.93[ASN][1000 genomes]
rs73186368	0.93[ASN][1000 genomes]
rs73186369	0.93[ASN][1000 genomes]
rs73186371	0.93[ASN][1000 genomes]
rs73186372	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73186374	0.93[ASN][1000 genomes]
rs73186376	0.93[ASN][1000 genomes]
rs73186381	0.93[ASN][1000 genomes]
rs73186382	0.93[ASN][1000 genomes]
rs73186390	0.93[ASN][1000 genomes]
rs7331290	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7999515	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9316511	0.81[CHD][hapmap]
rs9535529	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535531	1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs9535533	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535538	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9568487	0.82[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11616524	RNASEH2B	cis	cerebellum	SCAN
rs11616524	RNASEH2B	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51491600-51551000	Weak transcription	Small Intestine	intestine
2	chr13:51503200-51549400	Weak transcription	Psoas Muscle	Psoas
3	chr13:51503600-51551800	Strong transcription	Dnd41	blood
4	chr13:51504400-51551800	Strong transcription	Fetal Thymus	thymus
5	chr13:51509800-51550200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr13:51513000-51552200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr13:51516400-51548800	Weak transcription	Gastric	stomach
8	chr13:51518000-51550400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr13:51518000-51551200	Weak transcription	Placenta	Placenta
10	chr13:51518600-51552000	Weak transcription	Fetal Brain Female	brain
11	chr13:51518800-51549000	Weak transcription	Fetal Intestine Small	intestine
12	chr13:51521400-51549000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:51523600-51555200	Weak transcription	HSMMtube	muscle
14	chr13:51523800-51550600	Weak transcription	HSMM	muscle
15	chr13:51524600-51548400	Weak transcription	NHDF-Ad	bronchial
16	chr13:51524600-51550400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr13:51524800-51552200	Weak transcription	Colonic Mucosa	Colon
18	chr13:51526200-51549000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr13:51526200-51550000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr13:51530600-51563400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:51532600-51551400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr13:51533400-51552200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr13:51535800-51563200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr13:51537000-51550600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr13:51537800-51552000	Strong transcription	Primary T cells from cord blood	blood
26	chr13:51539200-51565400	Weak transcription	Esophagus	oesophagus
27	chr13:51539600-51564600	Weak transcription	Brain Angular Gyrus	brain
28	chr13:51539600-51564800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:51539800-51548800	Weak transcription	Fetal Intestine Large	intestine
30	chr13:51539800-51550600	Weak transcription	Left Ventricle	heart
31	chr13:51539800-51551200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:51539800-51551600	Weak transcription	Aorta	Aorta
33	chr13:51539800-51551800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr13:51539800-51552400	Weak transcription	GM12878-XiMat	blood
35	chr13:51539800-51553200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr13:51539800-51553400	Weak transcription	Fetal Kidney	kidney
37	chr13:51539800-51555000	Weak transcription	Brain Hippocampus Middle	brain
38	chr13:51540200-51552400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr13:51540400-51552600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr13:51540600-51551200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr13:51540600-51559000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr13:51540800-51555800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr13:51541200-51553200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr13:51542000-51549000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr13:51542200-51565400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr13:51543000-51549600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr13:51543600-51548600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr13:51544000-51551800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:51544400-51548400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr13:51544400-51548800	Weak transcription	Spleen	Spleen

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