Variant report

Variant	rs3771244
Chromosome Location	chr2:20412197-20412198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20313389..20316167-chr2:20411646..20415090,3	MCF-7	breast:
2	chr2:20340564..20344464-chr2:20412010..20415688,4	MCF-7	breast:
3	chr17:59475738..59478096-chr2:20410813..20413668,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267280	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000121068	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	0.92[ASN][1000 genomes]
rs1106111	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11096648	0.89[ASN][1000 genomes]
rs11096649	0.89[ASN][1000 genomes]
rs11096650	0.90[ASN][1000 genomes]
rs12373772	0.84[ASN][1000 genomes]
rs12373819	0.84[ASN][1000 genomes]
rs12464428	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13415389	0.84[ASN][1000 genomes]
rs2002090	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2007340	0.89[ASN][1000 genomes]
rs3732162	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732163	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732164	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755300	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771227	0.85[ASN][1000 genomes]
rs3771229	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771232	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771233	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3771236	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771238	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771239	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771240	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771241	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771243	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771246	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771247	0.84[ASN][1000 genomes]
rs3821219	0.91[AMR][1000 genomes];0.97[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	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72785204	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72785206	0.94[AMR][1000 genomes];0.92[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:71 , 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	chr2:20398000-20412200	Weak transcription	NH-A	brain
4	chr2:20403200-20412600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:20403400-20412400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:20403800-20412400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:20404000-20413600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:20404000-20414000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:20404000-20422400	Weak transcription	Brain Germinal Matrix	brain
10	chr2:20404600-20420800	Enhancers	Stomach Mucosa	stomach
11	chr2:20405000-20415000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:20405200-20413000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:20405200-20413800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:20405200-20414200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:20405200-20414600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:20405800-20416200	Enhancers	Gastric	stomach
17	chr2:20406200-20412800	Enhancers	GM12878-XiMat	blood
18	chr2:20407200-20412200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:20407200-20413000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:20407800-20414800	Enhancers	Colonic Mucosa	Colon
21	chr2:20408000-20412400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:20408000-20412600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:20408600-20412200	Weak transcription	NHLF	lung
24	chr2:20408600-20414800	Enhancers	Placenta	Placenta
25	chr2:20408800-20412800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:20408800-20413000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:20408800-20413600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:20409200-20413000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:20409400-20414400	Weak transcription	Small Intestine	intestine
30	chr2:20409400-20414800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:20409800-20412600	Weak transcription	A549	lung
32	chr2:20409800-20413000	Enhancers	Liver	Liver
33	chr2:20409800-20414800	Weak transcription	Lung	lung
34	chr2:20410400-20416200	Genic enhancers	Fetal Intestine Small	intestine
35	chr2:20410600-20412600	Enhancers	K562	blood
36	chr2:20410600-20417400	Enhancers	Fetal Intestine Large	intestine
37	chr2:20410800-20412400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:20410800-20414800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:20410800-20415200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:20410800-20415400	Enhancers	H1 Cell Line	embryonic stem cell
41	chr2:20411000-20412200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:20411000-20415400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr2:20411200-20412800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:20411200-20413400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:20411200-20413600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:20411400-20412200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:20411400-20414600	Enhancers	Fetal Thymus	thymus
48	chr2:20411400-20414800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:20411600-20412200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:20411600-20412200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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