Variant report

Variant	rs1019357
Chromosome Location	chr2:205535918-205535919
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:205529750..205532118-chr2:205534862..205537646,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1016338	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10180873	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1019356	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1030087	0.83[EUR][1000 genomes]
rs11688854	0.80[EUR][1000 genomes]
rs12694008	0.80[EUR][1000 genomes]
rs12694009	0.80[EUR][1000 genomes]
rs12694010	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1549012	0.84[EUR][1000 genomes]
rs1549013	0.84[EUR][1000 genomes]
rs1549014	0.84[EUR][1000 genomes]
rs16836537	0.86[EUR][1000 genomes]
rs1861763	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032691	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2052348	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2111446	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160690	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2216321	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2335632	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335633	0.81[EUR][1000 genomes]
rs2335634	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856507	0.83[EUR][1000 genomes]
rs4140727	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4591325	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675472	0.83[EUR][1000 genomes]
rs57144931	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435250	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6722595	0.82[EUR][1000 genomes]
rs6742535	0.84[EUR][1000 genomes]
rs6758329	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73059069	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7573176	0.89[EUR][1000 genomes]
rs7577059	0.84[EUR][1000 genomes]
rs7593604	0.84[EUR][1000 genomes]
rs7594540	0.94[ASN][1000 genomes]
rs7600049	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[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
rs1019357	ALS2CR4	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:205520800-205542800	Weak transcription	Psoas Muscle	Psoas
2	chr2:205521000-205546200	Weak transcription	Aorta	Aorta
3	chr2:205528000-205546200	Weak transcription	Pancreas	Pancrea
4	chr2:205530400-205538000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:205531000-205538200	Weak transcription	Osteobl	bone
6	chr2:205531000-205538400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:205531200-205538400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:205531200-205545200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:205531600-205539000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:205531800-205537600	Weak transcription	Fetal Kidney	kidney
11	chr2:205531800-205538000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:205531800-205538200	Weak transcription	NHDF-Ad	bronchial
13	chr2:205532200-205537000	Enhancers	Liver	Liver
14	chr2:205532200-205539800	Enhancers	HUVEC	blood vessel
15	chr2:205533200-205537400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:205534200-205536000	Enhancers	HepG2	liver
17	chr2:205534800-205538200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:205534800-205538800	Weak transcription	NHLF	lung
19	chr2:205535000-205536200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:205535000-205536200	Weak transcription	A549	lung
21	chr2:205535000-205536400	Enhancers	Gastric	stomach
22	chr2:205535200-205536000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:205535200-205536200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr2:205535200-205538200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:205535200-205545200	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:205535400-205536000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr2:205535400-205536000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr2:205535400-205537400	Weak transcription	HSMM	muscle
29	chr2:205535400-205542200	Weak transcription	HSMMtube	muscle
30	chr2:205535400-205545600	Weak transcription	Fetal Lung	lung
31	chr2:205535600-205536000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:205535600-205536200	Enhancers	Ovary	ovary
33	chr2:205535600-205536400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:205535800-205536000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:205535800-205538200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:205535800-205538400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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