Variant report

Variant	rs3771240
Chromosome Location	chr2:20412686-20412687
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
ENSG00000267131	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000267280	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10175853	0.88[CEU][hapmap]
rs10192042	0.88[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap]
rs1043400	0.86[MEX][hapmap]
rs10495704	0.83[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs1106111	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs11096648	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11096649	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11096650	0.90[ASN][1000 genomes]
rs11888357	0.81[MEX][hapmap]
rs12373772	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12373819	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12464428	0.84[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs13415389	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2002090	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs2007340	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732163	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732164	0.82[CEU][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755300	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771227	0.81[ASN][1000 genomes]
rs3771229	0.90[ASN][1000 genomes]
rs3771232	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771233	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3771236	0.84[CEU][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771238	0.83[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771239	0.83[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771241	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771243	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771244	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771246	0.96[ASN][1000 genomes]
rs3771247	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821219	0.94[ASN][1000 genomes]
rs57938873	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59129757	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62109740	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62111433	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72785203	0.90[ASN][1000 genomes]
rs72785204	0.90[ASN][1000 genomes]
rs72785206	0.90[ASN][1000 genomes]
rs7558833	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs7563245	0.92[CEU][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs7585590	0.96[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9306890	0.88[CEU][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3771240	GEN1	cis	parietal	SCAN

Chromatin state (count:74 , 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	chr2:20405200-20413000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:20405200-20413800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:20405200-20414200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:20405200-20414600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:20405800-20416200	Enhancers	Gastric	stomach
13	chr2:20406200-20412800	Enhancers	GM12878-XiMat	blood
14	chr2:20407200-20413000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:20407800-20414800	Enhancers	Colonic Mucosa	Colon
16	chr2:20408600-20414800	Enhancers	Placenta	Placenta
17	chr2:20408800-20412800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:20408800-20413000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:20408800-20413600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:20409200-20413000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:20409400-20414400	Weak transcription	Small Intestine	intestine
22	chr2:20409400-20414800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:20409800-20413000	Enhancers	Liver	Liver
24	chr2:20409800-20414800	Weak transcription	Lung	lung
25	chr2:20410400-20416200	Genic enhancers	Fetal Intestine Small	intestine
26	chr2:20410600-20417400	Enhancers	Fetal Intestine Large	intestine
27	chr2:20410800-20414800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:20410800-20415200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:20410800-20415400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr2:20411000-20415400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr2:20411200-20412800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:20411200-20413400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:20411200-20413600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:20411400-20414600	Enhancers	Fetal Thymus	thymus
35	chr2:20411400-20414800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:20411600-20413400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:20411600-20413600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr2:20411600-20413800	Enhancers	Fetal Stomach	stomach
39	chr2:20411600-20414200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:20411600-20414600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr2:20411600-20414800	Transcr. at gene 5' and 3'	NHEK	skin
42	chr2:20411800-20413600	Enhancers	Spleen	Spleen
43	chr2:20411800-20413800	Enhancers	Fetal Lung	lung
44	chr2:20411800-20414400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:20411800-20414800	Enhancers	Placenta Amnion	Placenta Amnion
46	chr2:20412000-20412800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:20412000-20412800	Enhancers	Duodenum Mucosa	Duodenum
48	chr2:20412000-20413400	Enhancers	Pancreas	Pancrea
49	chr2:20412000-20413800	Enhancers	Fetal Kidney	kidney
50	chr2:20412000-20414000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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