Variant report

Variant	rs3771229
Chromosome Location	chr2:20419923-20419924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20301244..20303124-chr2:20419816..20421979,2	MCF-7	breast:
2	chr17:57152201..57154948-chr2:20418855..20421470,2	MCF-7	breast:
3	chr2:20414820..20416839-chr2:20419190..20421088,3	K562	blood:
4	chr2:20418331..20420755-chr21:46948637..46950137,2	MCF-7	breast:
5	chr2:20418255..20420764-chr20:52271543..52273696,2	MCF-7	breast:
6	chr2:20249888..20254017-chr2:20419396..20423263,3	MCF-7	breast:
7	chr2:20329860..20331531-chr2:20418864..20420895,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223734	Chromatin interaction
ENSG00000068697	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10192042	0.81[MEX][hapmap]
rs1043400	0.82[CEU][hapmap];0.81[MEX][hapmap]
rs10495704	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1106111	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096648	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11096649	0.94[ASN][1000 genomes]
rs11096650	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11888357	0.83[CEU][hapmap]
rs11895228	0.86[CEU][hapmap]
rs12373772	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12373819	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12464428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415389	0.90[ASN][1000 genomes]
rs2002090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007340	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2348703	0.83[CEU][hapmap]
rs3732162	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs3732163	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732164	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755300	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771227	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3771232	0.83[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs3771233	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs3771236	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771238	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771239	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771240	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs3771241	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771243	0.90[ASN][1000 genomes]
rs3771244	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771246	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771247	0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs3796066	0.83[CEU][hapmap]
rs3821218	0.87[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap]
rs3821219	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57938873	0.90[ASN][1000 genomes]
rs59129757	0.90[ASN][1000 genomes]
rs62109740	0.90[ASN][1000 genomes]
rs62111433	0.90[ASN][1000 genomes]
rs6748274	0.83[CEU][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap]
rs72785203	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785206	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563245	0.86[MEX][hapmap]
rs7585590	0.93[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.94[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	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
2	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
3	esv3374014	chr2:20416371-20420569	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20391800-20423200	Weak transcription	Right Atrium	heart
2	chr2:20404000-20422400	Weak transcription	Brain Germinal Matrix	brain
3	chr2:20404600-20420800	Enhancers	Stomach Mucosa	stomach
4	chr2:20412600-20420600	Weak transcription	NHLF	lung
5	chr2:20413200-20420600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:20413200-20423000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:20413400-20420600	Weak transcription	NH-A	brain
8	chr2:20413400-20421000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:20414000-20421400	Weak transcription	Hela-S3	cervix
10	chr2:20414200-20420200	Strong transcription	Fetal Stomach	stomach
11	chr2:20414200-20420400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:20414200-20423000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:20414600-20421000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:20414600-20421600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:20414800-20420200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:20414800-20420400	Genic enhancers	Placenta	Placenta
17	chr2:20414800-20420600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:20414800-20421600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:20415000-20420800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:20415000-20421000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:20415200-20422000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:20415600-20422200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:20415800-20423200	Weak transcription	Small Intestine	intestine
24	chr2:20416000-20420400	Enhancers	Lung	lung
25	chr2:20416000-20423800	Transcr. at gene 5' and 3'	NHEK	skin
26	chr2:20416200-20420000	Strong transcription	Fetal Intestine Small	intestine
27	chr2:20416200-20423200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:20417000-20420800	Enhancers	GM12878-XiMat	blood
29	chr2:20417200-20422000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:20417800-20420400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:20417800-20422800	Transcr. at gene 5' and 3'	HMEC	breast
32	chr2:20418000-20422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:20418200-20421000	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr2:20418400-20422400	Genic enhancers	HepG2	liver
35	chr2:20418600-20420600	Weak transcription	Fetal Lung	lung
36	chr2:20418600-20421000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:20418600-20421600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:20418600-20422000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:20418600-20422600	Weak transcription	Fetal Kidney	kidney
40	chr2:20418800-20420000	Weak transcription	Spleen	Spleen
41	chr2:20418800-20420600	Strong transcription	A549	lung
42	chr2:20418800-20421000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:20418800-20421800	Weak transcription	Fetal Brain Male	brain
44	chr2:20418800-20423000	Flanking Active TSS	Liver	Liver
45	chr2:20419000-20420600	Enhancers	Duodenum Mucosa	Duodenum
46	chr2:20419000-20421400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:20419200-20420600	Genic enhancers	Esophagus	oesophagus
48	chr2:20419200-20422600	Enhancers	Fetal Intestine Large	intestine
49	chr2:20419400-20420400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:20419400-20420800	Weak transcription	Rectal Mucosa Donor 31	rectum

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