Variant report

Variant	rs566255
Chromosome Location	chr11:63512565-63512566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63487925..63490016-chr11:63510540..63512690,2	K562	blood:
2	chr11:63507589..63509838-chr11:63512231..63514308,2	K562	blood:
3	chr11:63490375..63492771-chr11:63512457..63514550,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10897442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231545	0.86[YRI][hapmap]
rs1186605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186941	0.85[MEX][hapmap]
rs1404500	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17615385	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1789218	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2509744	0.85[MEX][hapmap]
rs2850617	0.82[AFR][1000 genomes]
rs2959872	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959880	0.85[MEX][hapmap]
rs3016865	0.85[MEX][hapmap]
rs3758647	1.00[CHB][hapmap]
rs41509648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs474548	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500991	0.85[MEX][hapmap]
rs517700	0.85[MEX][hapmap]
rs520908	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs522648	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523093	0.85[MEX][hapmap]
rs542966	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542998	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545539	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567756	0.85[MEX][hapmap]
rs580083	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580695	0.85[MEX][hapmap]
rs61886075	0.81[EUR][1000 genomes]
rs61928249	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928251	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111395	0.85[MEX][hapmap]
rs7113325	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121664	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7122132	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7128970	0.85[MEX][hapmap]
rs7943981	0.85[MEX][hapmap]
rs7945972	0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv832183	chr11:63416678-63564565	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs566255	HRASLS3	cis	multi-tissue	Pritchard
rs566255	SNORD25	cis	parietal	SCAN
rs566255	PLA2G16	cis	cerebellum	SCAN
rs566255	RASGRP2	cis	parietal	SCAN
rs566255	MTA2	cis	cerebellum	SCAN
rs566255	NAA40	cis	cerebellum	SCAN
rs566255	FLRT1	cis	cerebellum	SCAN
rs566255	ANKRD13D	cis	cerebellum	SCAN
rs566255	SAC3D1	cis	cerebellum	SCAN
rs566255	SLC22A9	cis	cerebellum	SCAN
rs566255	GNG3	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63450800-63517400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr11:63459600-63516600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:63463200-63516200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:63467600-63516000	Weak transcription	Thymus	Thymus
5	chr11:63467600-63517600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:63473000-63516000	Weak transcription	Lung	lung
7	chr11:63473000-63518000	Weak transcription	Aorta	Aorta
8	chr11:63473000-63529400	Weak transcription	Right Ventricle	heart
9	chr11:63478800-63517200	Weak transcription	Fetal Intestine Small	intestine
10	chr11:63481000-63517600	Weak transcription	Spleen	Spleen
11	chr11:63481800-63512800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:63483400-63517000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:63486200-63519200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:63487000-63516800	Weak transcription	Primary T cells from cord blood	blood
15	chr11:63487400-63516000	Weak transcription	Fetal Thymus	thymus
16	chr11:63487400-63516600	Weak transcription	Dnd41	blood
17	chr11:63487400-63517000	Weak transcription	Fetal Muscle Leg	muscle
18	chr11:63487400-63517600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:63487600-63513400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:63487800-63516600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:63488000-63516600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:63488000-63519800	Weak transcription	NH-A	brain
23	chr11:63488400-63516400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:63488400-63516400	Weak transcription	Brain Germinal Matrix	brain
25	chr11:63491000-63529600	Weak transcription	Pancreas	Pancrea
26	chr11:63492800-63528000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:63494600-63516200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:63497800-63514800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:63499000-63518600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:63501800-63518400	Weak transcription	Fetal Brain Female	brain
31	chr11:63501800-63530000	Weak transcription	Psoas Muscle	Psoas
32	chr11:63502000-63516200	Weak transcription	Fetal Stomach	stomach
33	chr11:63502000-63516800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr11:63505600-63516600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr11:63505600-63517200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:63506000-63513600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:63506200-63516600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:63506200-63517200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:63506200-63517600	Weak transcription	Colon Smooth Muscle	Colon
40	chr11:63506200-63527600	Weak transcription	Fetal Brain Male	brain
41	chr11:63506400-63512800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:63506400-63512800	Weak transcription	Brain Anterior Caudate	brain
43	chr11:63506400-63512800	Weak transcription	HepG2	liver
44	chr11:63506400-63513200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:63506400-63514400	Weak transcription	NHDF-Ad	bronchial
46	chr11:63506400-63516400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:63506400-63516400	Weak transcription	A549	lung
48	chr11:63506400-63516600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:63506400-63517200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:63506400-63517400	Weak transcription	Primary hematopoietic stem cells	blood

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