Variant report

Variant	rs3828260
Chromosome Location	chr2:10094442-10094443
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10091739..10097867-chr2:10098252..10106254,13	K562	blood:
2	chr2:9937659..9941164-chr2:10094129..10096263,3	MCF-7	breast:
3	chr2:10092110..10094474-chr2:10182208..10184991,2	K562	blood:
4	chr2:9932897..9935597-chr2:10092783..10094532,2	MCF-7	breast:
5	chr2:9938284..9940065-chr2:10092605..10094538,2	MCF-7	breast:
6	chr2:9983066..9987186-chr2:10091615..10095343,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172059	Chromatin interaction
ENSG00000115750	Chromatin interaction
ENSG00000134317	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1001215	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12470881	0.87[CHB][hapmap]
rs12472800	0.82[AMR][1000 genomes]
rs12616347	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12618788	0.87[CHB][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs12623004	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs13009358	0.86[ASN][1000 genomes]
rs1367383	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs1367388	0.92[CHB][hapmap]
rs1367389	0.92[CHB][hapmap]
rs1549752	0.80[ASN][1000 genomes]
rs1549753	0.93[CHB][hapmap]
rs1549754	0.93[CHB][hapmap]
rs1820964	0.80[ASN][1000 genomes]
rs1864539	0.83[MEX][hapmap]
rs1897165	0.80[ASN][1000 genomes]
rs2011516	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs2011523	0.80[ASN][1000 genomes]
rs2033324	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2033325	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2033326	0.80[ASN][1000 genomes]
rs2303920	0.93[CHB][hapmap]
rs28444564	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34629102	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34950562	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35321554	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35341467	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35646916	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35816086	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36033432	0.80[ASN][1000 genomes]
rs3762536	0.85[CEU][hapmap];0.93[CHD][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3762537	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3762538	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3791753	0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3791758	0.80[ASN][1000 genomes]
rs3791760	0.82[JPT][hapmap]
rs4669508	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4669511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432047	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs6432048	0.80[ASN][1000 genomes]
rs72784422	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72784424	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72784425	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs731453	0.93[CHB][hapmap]
rs891500	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3828260	CYS1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10092200-10095600	Bivalent Enhancer	Fetal Lung	lung
2	chr2:10092600-10094600	Weak transcription	Gastric	stomach
3	chr2:10092600-10104200	Weak transcription	Lung	lung
4	chr2:10092600-10112600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:10092600-10113400	Weak transcription	Left Ventricle	heart
6	chr2:10092800-10094600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:10092800-10101000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:10092800-10101200	Weak transcription	Brain Angular Gyrus	brain
9	chr2:10092800-10110600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:10093200-10095800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:10093200-10101200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:10093200-10105600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:10093200-10110600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:10093400-10100800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:10093600-10094800	Bivalent Enhancer	Brain Germinal Matrix	brain
16	chr2:10093600-10095000	Enhancers	HepG2	liver
17	chr2:10093600-10100600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:10093600-10100600	Weak transcription	K562	blood
19	chr2:10093600-10104400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:10093600-10112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:10093800-10094600	Enhancers	Liver	Liver
22	chr2:10094000-10095400	Weak transcription	Placenta	Placenta
23	chr2:10094000-10098800	Weak transcription	Adipose Nuclei	Adipose
24	chr2:10094000-10101000	Weak transcription	Dnd41	blood
25	chr2:10094400-10094600	Flanking Active TSS	Hela-S3	cervix
26	chr2:10094400-10094800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:10094400-10094800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:10094400-10094800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:10094400-10094800	Enhancers	Duodenum Mucosa	Duodenum
30	chr2:10094400-10094800	Enhancers	Fetal Intestine Large	intestine
31	chr2:10094400-10094800	Enhancers	Fetal Intestine Small	intestine
32	chr2:10094400-10094800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
33	chr2:10094400-10094800	Enhancers	NHDF-Ad	bronchial
34	chr2:10094400-10095000	Enhancers	Pancreas	Pancrea
35	chr2:10094400-10095000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
36	chr2:10094400-10096000	Active TSS	Esophagus	oesophagus

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