Variant report

Variant	rs1861763
Chromosome Location	chr2:205528990-205528991
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	chr2:205528626..205531544-chr2:205538166..205540869,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1016338	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10180873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10186433	0.81[EUR][1000 genomes]
rs1019356	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1019357	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205296	0.84[EUR][1000 genomes]
rs1030087	0.80[EUR][1000 genomes]
rs11677461	0.84[EUR][1000 genomes]
rs11688854	0.84[EUR][1000 genomes]
rs11691772	0.84[EUR][1000 genomes]
rs11693425	0.84[EUR][1000 genomes]
rs11893764	0.83[EUR][1000 genomes]
rs11899398	0.82[EUR][1000 genomes]
rs12694008	0.84[EUR][1000 genomes]
rs12694009	0.84[EUR][1000 genomes]
rs12694010	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1549012	0.80[EUR][1000 genomes]
rs1549013	0.80[EUR][1000 genomes]
rs16836537	0.84[EUR][1000 genomes]
rs2032691	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2052348	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2080601	0.84[EUR][1000 genomes]
rs2098461	0.84[EUR][1000 genomes]
rs2111446	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160689	0.84[EUR][1000 genomes]
rs2160690	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2216321	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2335632	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335633	0.85[EUR][1000 genomes]
rs2335634	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856507	0.80[EUR][1000 genomes]
rs4140727	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4591325	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675472	0.80[EUR][1000 genomes]
rs57144931	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435250	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6722595	0.82[EUR][1000 genomes]
rs6751181	0.80[EUR][1000 genomes]
rs6758329	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73059069	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7573176	0.86[EUR][1000 genomes]
rs7594540	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7600049	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998485	chr2:205407813-206184006	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536122	chr2:205407813-206184006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875722	chr2:205462099-205572718	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv875723	chr2:205489653-205612846	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1010210	chr2:205489653-206076013	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1861763	ALS2CR4	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:205507400-205530000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:205517200-205530000	Weak transcription	Ovary	ovary
3	chr2:205519400-205529400	Weak transcription	Fetal Heart	heart
4	chr2:205520000-205529200	Weak transcription	Fetal Lung	lung
5	chr2:205520200-205529200	Weak transcription	Esophagus	oesophagus
6	chr2:205520800-205542800	Weak transcription	Psoas Muscle	Psoas
7	chr2:205521000-205546200	Weak transcription	Aorta	Aorta
8	chr2:205521800-205529000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:205522200-205530000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:205525400-205529000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:205527800-205529600	Enhancers	NHDF-Ad	bronchial
12	chr2:205527800-205531400	Enhancers	HSMM	muscle
13	chr2:205527800-205531800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:205527800-205533200	Enhancers	HSMMtube	muscle
15	chr2:205528000-205530000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:205528000-205546200	Weak transcription	Pancreas	Pancrea
17	chr2:205528200-205529000	Enhancers	Stomach Mucosa	stomach
18	chr2:205528200-205530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:205528400-205532800	Weak transcription	Gastric	stomach
20	chr2:205528600-205529400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:205528600-205529400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:205528600-205529800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr2:205528600-205531000	Enhancers	NHLF	lung
24	chr2:205528600-205531200	Enhancers	Colon Smooth Muscle	Colon
25	chr2:205528800-205529600	Enhancers	NHEK	skin
26	chr2:205528800-205530400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:205528800-205530600	Flanking Active TSS	A549	lung
28	chr2:205528800-205530800	Enhancers	Hela-S3	cervix
29	chr2:205528800-205531000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:205528800-205531000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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