Variant report

Variant	rs3732163
Chromosome Location	chr2:20413454-20413455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20332825..20334861-chr2:20412416..20414197,2	MCF-7	breast:
2	chr2:20313389..20316167-chr2:20411646..20415090,3	MCF-7	breast:
3	chr2:20340564..20344464-chr2:20412010..20415688,4	MCF-7	breast:
4	chr17:59475738..59478096-chr2:20410813..20413668,2	MCF-7	breast:
5	chr2:20271585..20273476-chr2:20412468..20414471,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121068	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000267131	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10495704	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1106111	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11096648	0.89[ASN][1000 genomes]
rs11096649	0.89[ASN][1000 genomes]
rs11096650	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12373772	0.84[ASN][1000 genomes]
rs12373819	0.84[ASN][1000 genomes]
rs12464428	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13415389	0.84[ASN][1000 genomes]
rs2002090	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2007340	0.89[ASN][1000 genomes]
rs3732162	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732164	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755300	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771227	0.85[ASN][1000 genomes]
rs3771229	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771232	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771233	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3771236	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771238	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771239	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771240	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771241	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771243	0.96[ASN][1000 genomes]
rs3771244	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771246	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771247	0.84[ASN][1000 genomes]
rs3821219	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57938873	0.84[ASN][1000 genomes]
rs59129757	0.84[ASN][1000 genomes]
rs62109740	0.84[ASN][1000 genomes]
rs62111433	0.84[ASN][1000 genomes]
rs72785203	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72785204	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72785206	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7585590	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1846803	chr2:20409322-20427189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20389200-20413600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:20391800-20423200	Weak transcription	Right Atrium	heart
3	chr2:20404000-20413600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:20404000-20414000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:20404000-20422400	Weak transcription	Brain Germinal Matrix	brain
6	chr2:20404600-20420800	Enhancers	Stomach Mucosa	stomach
7	chr2:20405000-20415000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:20405200-20413800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:20405200-20414200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:20405200-20414600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:20405800-20416200	Enhancers	Gastric	stomach
12	chr2:20407800-20414800	Enhancers	Colonic Mucosa	Colon
13	chr2:20408600-20414800	Enhancers	Placenta	Placenta
14	chr2:20408800-20413600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:20409400-20414400	Weak transcription	Small Intestine	intestine
16	chr2:20409400-20414800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:20409800-20414800	Weak transcription	Lung	lung
18	chr2:20410400-20416200	Genic enhancers	Fetal Intestine Small	intestine
19	chr2:20410600-20417400	Enhancers	Fetal Intestine Large	intestine
20	chr2:20410800-20414800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:20410800-20415200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:20410800-20415400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr2:20411000-20415400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr2:20411200-20413600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:20411400-20414600	Enhancers	Fetal Thymus	thymus
26	chr2:20411400-20414800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:20411600-20413600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr2:20411600-20413800	Enhancers	Fetal Stomach	stomach
29	chr2:20411600-20414200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:20411600-20414600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr2:20411600-20414800	Transcr. at gene 5' and 3'	NHEK	skin
32	chr2:20411800-20413600	Enhancers	Spleen	Spleen
33	chr2:20411800-20413800	Enhancers	Fetal Lung	lung
34	chr2:20411800-20414400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:20411800-20414800	Enhancers	Placenta Amnion	Placenta Amnion
36	chr2:20412000-20413800	Enhancers	Fetal Kidney	kidney
37	chr2:20412000-20414000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:20412000-20414400	Flanking Active TSS	HMEC	breast
39	chr2:20412000-20415000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:20412200-20413600	Enhancers	Fetal Muscle Leg	muscle
41	chr2:20412200-20414200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:20412400-20413600	Enhancers	Ovary	ovary
43	chr2:20412400-20414200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr2:20412400-20416000	Flanking Active TSS	HepG2	liver
45	chr2:20412600-20414800	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr2:20412600-20415400	Enhancers	A549	lung
47	chr2:20412600-20420600	Weak transcription	NHLF	lung
48	chr2:20412800-20413800	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr2:20412800-20414000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:20412800-20414000	Flanking Active TSS	GM12878-XiMat	blood

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