Variant report

Variant	rs2843014
Chromosome Location	chr1:120328527-120328528
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	chr1:120327792..120331105-chr1:120334813..120337801,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1163542	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1163543	0.99[EUR][1000 genomes]
rs1163544	0.99[EUR][1000 genomes]
rs1163550	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1177389	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123085	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12132674	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1660607	1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1814447	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582779	1.00[EUR][1000 genomes]
rs2582780	0.99[EUR][1000 genomes]
rs2582782	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2582784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2582785	0.90[CEU][hapmap];0.97[EUR][1000 genomes]
rs2582786	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582790	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap];0.98[EUR][1000 genomes]
rs2843015	1.00[CEU][hapmap];0.80[GIH][hapmap];0.92[TSI][hapmap];0.99[EUR][1000 genomes]
rs2843016	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2843017	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56239558	0.89[ASN][1000 genomes]
rs61789690	0.85[ASN][1000 genomes]
rs72695189	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs753425	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930448	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935060	0.98[EUR][1000 genomes]
rs978730	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2843014	CD2	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120321600-120330800	Enhancers	Placenta	Placenta
2	chr1:120323600-120329400	Enhancers	Liver	Liver
3	chr1:120323800-120332600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:120324600-120328800	Enhancers	HepG2	liver
5	chr1:120324800-120328800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:120324800-120329000	Enhancers	Fetal Stomach	stomach
7	chr1:120324800-120330600	Enhancers	Fetal Muscle Leg	muscle
8	chr1:120324800-120330800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:120324800-120331000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr1:120324800-120335000	Enhancers	Fetal Intestine Large	intestine
11	chr1:120324800-120335000	Enhancers	Fetal Intestine Small	intestine
12	chr1:120325000-120328800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:120325000-120328800	Enhancers	Fetal Lung	lung
14	chr1:120325200-120331000	Enhancers	HMEC	breast
15	chr1:120325400-120330000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:120325400-120331600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:120325600-120333600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:120326200-120328600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:120326400-120329000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:120326600-120330400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:120326800-120330000	Weak transcription	Pancreas	Pancrea
22	chr1:120326800-120330600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:120327000-120330400	Weak transcription	Fetal Kidney	kidney
24	chr1:120327200-120329400	Weak transcription	Small Intestine	intestine
25	chr1:120327200-120330000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:120327200-120336400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:120327400-120329400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:120327400-120337000	Weak transcription	Colonic Mucosa	Colon
29	chr1:120327800-120328600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:120328000-120328600	Enhancers	HSMMtube	muscle
31	chr1:120328000-120329000	Enhancers	Gastric	stomach
32	chr1:120328000-120331000	Enhancers	Stomach Mucosa	stomach
33	chr1:120328000-120331200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:120328200-120328800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:120328200-120328800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr1:120328200-120329400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:120328200-120331200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:120328400-120329400	Weak transcription	Esophagus	oesophagus
39	chr1:120328400-120329400	Weak transcription	Lung	lung
40	chr1:120328400-120329400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:120328400-120330200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:120328400-120330800	Enhancers	NHEK	skin
43	chr1:120328400-120336800	Weak transcription	Fetal Muscle Trunk	muscle

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