Variant report

Variant	rs2582779
Chromosome Location	chr1:120332045-120332046
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:120329924..120336261-chr1:120336777..120341772,6	K562	blood:
2	chr1:120330723..120332386-chr1:120334423..120336178,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1163542	0.99[EUR][1000 genomes]
rs1163543	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1163544	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1163550	0.99[EUR][1000 genomes]
rs1177389	1.00[EUR][1000 genomes]
rs12132674	0.87[CEU][hapmap];0.95[EUR][1000 genomes]
rs1814447	0.98[EUR][1000 genomes]
rs2282402	0.80[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2582780	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582782	1.00[EUR][1000 genomes]
rs2582784	1.00[CEU][hapmap]
rs2582785	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2582786	0.89[CEU][hapmap];0.98[EUR][1000 genomes]
rs2582790	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2843014	1.00[EUR][1000 genomes]
rs2843015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2843016	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs2843017	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs72695189	0.97[EUR][1000 genomes]
rs753425	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs930448	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs935060	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978730	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2582779	CD2	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120323800-120332600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:120324800-120335000	Enhancers	Fetal Intestine Large	intestine
3	chr1:120324800-120335000	Enhancers	Fetal Intestine Small	intestine
4	chr1:120325600-120333600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:120327200-120336400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:120327400-120337000	Weak transcription	Colonic Mucosa	Colon
7	chr1:120328400-120336800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:120328600-120333200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:120328800-120333200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:120328800-120333600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:120329000-120332800	Weak transcription	Fetal Stomach	stomach
12	chr1:120329600-120333600	Weak transcription	Gastric	stomach
13	chr1:120330000-120334400	Enhancers	Duodenum Mucosa	Duodenum
14	chr1:120330200-120332800	Weak transcription	Small Intestine	intestine
15	chr1:120330200-120333600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:120330200-120336000	Weak transcription	Esophagus	oesophagus
17	chr1:120330600-120333200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:120330600-120333600	Weak transcription	Pancreas	Pancrea
19	chr1:120330600-120336000	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:120330800-120332800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:120330800-120333200	Weak transcription	Placenta	Placenta
22	chr1:120330800-120335800	Weak transcription	Fetal Lung	lung
23	chr1:120331000-120332800	Weak transcription	Stomach Mucosa	stomach
24	chr1:120331000-120335800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:120331000-120337800	Weak transcription	HMEC	breast
26	chr1:120331200-120332600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:120331200-120332800	Weak transcription	HepG2	liver
28	chr1:120331200-120333000	Weak transcription	Fetal Kidney	kidney
29	chr1:120331200-120333200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:120331200-120336200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:120331600-120332600	Weak transcription	Liver	Liver
32	chr1:120331600-120333800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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