Variant report

Variant	rs2843016
Chromosome Location	chr1:120322961-120322962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120254317..120256154-chr1:120322283..120325214,2	MCF-7	breast:
2	chr1:120312850..120316176-chr1:120320921..120324121,3	MCF-7	breast:
3	chr1:120276233..120278841-chr1:120322677..120325255,2	K562	blood:
4	chr1:120318567..120320764-chr1:120321980..120324094,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1163542	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1163543	0.98[EUR][1000 genomes]
rs1163544	0.97[EUR][1000 genomes]
rs1163550	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1177389	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1660607	1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1814447	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582779	0.99[EUR][1000 genomes]
rs2582780	0.98[EUR][1000 genomes]
rs2582782	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.99[EUR][1000 genomes]
rs2582786	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582790	0.96[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs2843014	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2843015	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2843017	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.95[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];0.99[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935060	0.99[EUR][1000 genomes]
rs978730	0.97[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2843016	CD2	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120311800-120324800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:120311800-120325400	Weak transcription	Lung	lung
3	chr1:120314600-120324800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:120316800-120326000	Weak transcription	Esophagus	oesophagus
5	chr1:120317000-120325400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:120318400-120325200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:120318400-120328000	Weak transcription	Gastric	stomach
8	chr1:120321600-120323800	Enhancers	Fetal Intestine Small	intestine
9	chr1:120321600-120330800	Enhancers	Placenta	Placenta
10	chr1:120321800-120323000	Enhancers	Fetal Intestine Large	intestine
11	chr1:120321800-120323200	Enhancers	Fetal Stomach	stomach
12	chr1:120321800-120323200	Flanking Active TSS	HepG2	liver
13	chr1:120322000-120323000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:120322000-120323000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:120322000-120323000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:120322000-120323600	Flanking Active TSS	Liver	Liver
17	chr1:120322000-120323800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr1:120322200-120323000	Enhancers	Fetal Heart	heart
19	chr1:120322200-120323200	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr1:120322400-120323000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:120322400-120323000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:120322400-120323000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:120322400-120323000	Flanking Active TSS	Stomach Mucosa	stomach
24	chr1:120322400-120323000	Flanking Active TSS	Hela-S3	cervix
25	chr1:120322400-120323200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:120322400-120323400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:120322600-120323000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:120322600-120323000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:120322600-120323000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:120322600-120323000	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr1:120322600-120323000	Active TSS	Colon Smooth Muscle	Colon
32	chr1:120322600-120323000	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:120322600-120323000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr1:120322600-120323000	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr1:120322600-120323000	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr1:120322600-120323000	Flanking Active TSS	Right Atrium	heart
37	chr1:120322600-120323000	Flanking Active TSS	HSMMtube	muscle
38	chr1:120322600-120323000	Flanking Active TSS	NHDF-Ad	bronchial
39	chr1:120322600-120323000	Flanking Active TSS	NHEK	skin
40	chr1:120322600-120323000	Active TSS	NHLF	lung
41	chr1:120322600-120323200	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr1:120322600-120323400	Flanking Active TSS	Fetal Kidney	kidney
43	chr1:120322600-120323400	Flanking Active TSS	Fetal Lung	lung
44	chr1:120322600-120323400	Enhancers	Pancreas	Pancrea
45	chr1:120322600-120323800	Enhancers	HSMM	muscle
46	chr1:120322800-120323000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:120322800-120323000	Active TSS	Stomach Smooth Muscle	stomach
48	chr1:120322800-120323200	Active TSS	Duodenum Mucosa	Duodenum
49	chr1:120322800-120323200	Active TSS	Ovary	ovary
50	chr1:120322800-120325200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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