Variant report

Variant	rs11753205
Chromosome Location	chr6:80252423-80252424
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:80251123..80253109-chr6:80259738..80262557,2	K562	blood:
2	chr6:80246201..80249127-chr6:80252156..80255932,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261970	Chromatin interaction
ENSG00000135338	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10484941	0.89[MEX][hapmap]
rs11756302	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11756486	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11757993	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11758791	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1472729	1.00[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16879583	0.86[ASN][1000 genomes]
rs16890791	0.90[CHB][hapmap];1.00[CHD][hapmap]
rs16890821	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16890842	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16890846	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1857722	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2047897	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2069304	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2455943	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2455944	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2655665	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2655686	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2655689	1.00[CEU][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2655693	0.81[CEU][hapmap]
rs2803172	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2803176	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2803177	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2803178	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2803179	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2812697	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2812699	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34068461	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4706790	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4706791	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4706792	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55697211	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55951062	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56311322	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72899927	0.86[ASN][1000 genomes]
rs72899942	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72899955	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72901812	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72901839	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7742272	0.80[CHD][hapmap]
rs7743617	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7755562	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7771276	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7774418	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7775536	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9443675	0.87[ASN][1000 genomes]
rs9448731	0.87[ASN][1000 genomes]
rs9448733	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9448738	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv886303	chr6:80147225-80252423	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv463906	chr6:80240951-80313297	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv604052	chr6:80240951-80313297	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11753205	LCA5	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80247600-80267800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:80247800-80253800	Weak transcription	Small Intestine	intestine
3	chr6:80247800-80256800	Weak transcription	Lung	lung
4	chr6:80247800-80257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:80247800-80257000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:80247800-80257600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:80248000-80262000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:80248200-80253600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:80248600-80254000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:80248600-80254000	Weak transcription	Primary T cells from cord blood	blood
11	chr6:80248600-80254000	Weak transcription	Hela-S3	cervix
12	chr6:80248600-80262800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:80248600-80262800	Weak transcription	Liver	Liver
14	chr6:80248800-80252600	Weak transcription	GM12878-XiMat	blood
15	chr6:80248800-80253000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:80248800-80253200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:80248800-80253200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:80248800-80253200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:80248800-80253200	Weak transcription	NHLF	lung
20	chr6:80248800-80253400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:80248800-80253600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:80248800-80253600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:80248800-80253600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr6:80248800-80253600	Weak transcription	HSMMtube	muscle
25	chr6:80248800-80253800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:80248800-80253800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:80248800-80253800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:80248800-80253800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:80248800-80253800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:80248800-80253800	Weak transcription	Fetal Kidney	kidney
31	chr6:80248800-80253800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:80248800-80253800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:80248800-80254000	Weak transcription	Adipose Nuclei	Adipose
34	chr6:80248800-80254000	Weak transcription	Fetal Brain Male	brain
35	chr6:80248800-80254000	Weak transcription	Fetal Intestine Small	intestine
36	chr6:80248800-80254000	Weak transcription	Right Ventricle	heart
37	chr6:80248800-80254000	Weak transcription	NHDF-Ad	bronchial
38	chr6:80248800-80254600	Weak transcription	Aorta	Aorta
39	chr6:80248800-80257000	Weak transcription	Pancreas	Pancrea
40	chr6:80248800-80258000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:80248800-80262000	Weak transcription	Psoas Muscle	Psoas
42	chr6:80248800-80272000	Weak transcription	Ovary	ovary
43	chr6:80249000-80253000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr6:80249000-80253000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:80249000-80253000	Weak transcription	NH-A	brain
46	chr6:80249000-80253800	Weak transcription	Osteobl	bone
47	chr6:80249200-80253000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:80249200-80253600	Weak transcription	HUVEC	blood vessel
49	chr6:80249400-80253000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:80249400-80253400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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