Variant report

Variant	rs1149613
Chromosome Location	chr11:76497432-76497433
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr11:76495697-76498146	A549	lung:	n/a	chr11:76497573-76497581
2	POLR2A	chr11:76497049-76497900	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:76491728-76497876	HepG2	liver:	n/a	n/a
4	SP1	chr11:76496985-76497586	A549	lung:	n/a	n/a
5	MAX	chr11:76491870-76500240	A549	lung:	n/a	chr11:76495789-76495799 chr11:76494160-76494170 chr11:76494949-76494959 chr11:76499004-76499014 chr11:76494703-76494719 chr11:76500087-76500096
6	BCL3	chr11:76496983-76498006	A549	lung:	n/a	chr11:76497573-76497581
7	TCF12	chr11:76491706-76499377	A549	lung:	n/a	chr11:76495264-76495274 chr11:76499211-76499221 chr11:76492154-76492161 chr11:76499346-76499356 chr11:76492802-76492812
8	FOSL2	chr11:76495934-76497552	A549	lung:	n/a	n/a
9	POLR2A	chr11:76497011-76497438	A549	lung:	n/a	n/a
10	POLR2A	chr11:76497001-76500285	A549	lung:	n/a	n/a
11	POLR2A	chr11:76494484-76500840	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:76493164..76499691-chr11:76510608..76517041,14	MCF-7	breast:
2	chr11:76449564..76451543-chr11:76496131..76497754,2	MCF-7	breast:
3	chr11:76482203..76483878-chr11:76496457..76499496,3	K562	blood:
4	chr11:76496902..76499372-chr11:76570017..76571527,2	K562	blood:
5	chr11:76492689..76500449-chr11:76507700..76515545,17	K562	blood:
6	chr11:76497234..76499501-chr11:76534793..76537709,2	K562	blood:

Variant related genes	Relation type
ENSG00000255100	TF binding region
ENSG00000261578	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1149595	0.85[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1149600	0.88[EUR][1000 genomes]
rs1149602	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1149603	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1149611	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1149620	0.84[EUR][1000 genomes]
rs1224953	0.88[ASN][1000 genomes]
rs1224954	0.88[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs876361	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897931	chr11:76489673-76540708	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1149613	P2RY6	cis	parietal	SCAN
rs1149613	RP11-21L23.4	cis	Adipose Subcutaneous	GTEx
rs1149613	RP11-672A2.1	cis	Adipose Subcutaneous	GTEx
rs1149613	PAAF1	cis	parietal	SCAN
rs1149613	SNORD15B	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76495000-76498000	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr11:76495400-76501800	Transcr. at gene 5' and 3'	A549	lung
3	chr11:76495600-76497800	Flanking Active TSS	Fetal Brain Female	brain
4	chr11:76495600-76497800	Enhancers	Spleen	Spleen
5	chr11:76495800-76498000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:76495800-76499600	Weak transcription	Brain Substantia Nigra	brain
7	chr11:76496000-76497800	Flanking Active TSS	Liver	Liver
8	chr11:76496000-76497800	Enhancers	Fetal Lung	lung
9	chr11:76496000-76497800	Transcr. at gene 5' and 3'	Hela-S3	cervix
10	chr11:76496000-76499000	Weak transcription	Lung	lung
11	chr11:76496000-76499200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:76496000-76499400	Weak transcription	Brain Anterior Caudate	brain
13	chr11:76496000-76499600	Weak transcription	Brain Angular Gyrus	brain
14	chr11:76496000-76499800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:76496000-76500600	Enhancers	Fetal Muscle Trunk	muscle
16	chr11:76496000-76501000	Enhancers	Right Ventricle	heart
17	chr11:76496000-76506800	Weak transcription	Aorta	Aorta
18	chr11:76496200-76498000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:76496200-76498200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:76496200-76498200	Enhancers	Fetal Muscle Leg	muscle
21	chr11:76496200-76498600	Enhancers	Brain Hippocampus Middle	brain
22	chr11:76496200-76499400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:76496200-76499800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr11:76496200-76503600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:76496200-76513800	Weak transcription	Fetal Kidney	kidney
26	chr11:76496400-76497800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:76496400-76498000	Enhancers	Fetal Brain Male	brain
28	chr11:76496400-76498000	Enhancers	Placenta	Placenta
29	chr11:76496400-76498200	Enhancers	K562	blood
30	chr11:76496400-76500600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:76496400-76500600	Enhancers	Fetal Heart	heart
32	chr11:76496400-76501000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:76496400-76501800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr11:76496400-76504000	Weak transcription	HSMMtube	muscle
35	chr11:76496600-76497600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr11:76496600-76497600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr11:76496600-76498200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:76496600-76498200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:76496600-76498200	Enhancers	NHDF-Ad	bronchial
40	chr11:76496600-76498200	Enhancers	Osteobl	bone
41	chr11:76496600-76498400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr11:76496600-76498800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr11:76496600-76499200	Weak transcription	NH-A	brain
44	chr11:76496600-76500400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:76496600-76500800	Enhancers	Pancreas	Pancrea
46	chr11:76496600-76504400	Weak transcription	HUVEC	blood vessel
47	chr11:76496600-76509800	Weak transcription	Colon Smooth Muscle	Colon
48	chr11:76496800-76497600	Enhancers	Esophagus	oesophagus
49	chr11:76496800-76497800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:76496800-76498000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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