Variant report

Variant	rs2802269
Chromosome Location	chr1:227182033-227182034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227160421..227162343-chr1:227181472..227183178,2	MCF-7	breast:
2	chr1:227129636..227132325-chr1:227181300..227183713,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12035998	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1289470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1298652	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1888826	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1888828	0.91[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2490269	0.91[CEU][hapmap];0.86[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2777833	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2777841	1.00[JPT][hapmap]
rs2777842	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2777843	1.00[ASW][hapmap];0.81[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2997438	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806262	1.00[ASW][hapmap];0.81[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4653476	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4653477	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4653780	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs533134	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs6664803	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:227173400-227183400	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:227175200-227198400	Weak transcription	A549	lung
6	chr1:227175200-227210200	Weak transcription	HMEC	breast
7	chr1:227175400-227182600	Genic enhancers	Fetal Intestine Small	intestine
8	chr1:227175600-227182200	Weak transcription	Brain Germinal Matrix	brain
9	chr1:227175600-227183200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:227176000-227190200	Weak transcription	Esophagus	oesophagus
12	chr1:227176000-227191800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:227176000-227216400	Weak transcription	NHLF	lung
14	chr1:227176400-227190400	Weak transcription	Osteobl	bone
15	chr1:227176600-227182400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:227176600-227190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:227177200-227188600	Weak transcription	Fetal Lung	lung
18	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
19	chr1:227178000-227183200	Strong transcription	Fetal Stomach	stomach
20	chr1:227178200-227183000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:227178200-227188600	Weak transcription	HSMMtube	muscle
22	chr1:227178400-227182200	Weak transcription	Brain Anterior Caudate	brain
23	chr1:227178400-227190400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
25	chr1:227178600-227182400	Weak transcription	GM12878-XiMat	blood
26	chr1:227178600-227206600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:227178800-227183000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:227178800-227188800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:227179000-227182800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:227179000-227188400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:227179400-227183000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:227179400-227183200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:227179400-227188200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:227179400-227198400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:227179400-227204400	Weak transcription	Stomach Mucosa	stomach
37	chr1:227179400-227215000	Weak transcription	Placenta	Placenta
38	chr1:227179600-227213800	Weak transcription	NH-A	brain
39	chr1:227180000-227182600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:227180000-227183200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:227180200-227183200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:227180200-227184200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:227180400-227182200	Enhancers	Fetal Brain Male	brain
44	chr1:227180400-227182600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:227180400-227183000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:227180400-227184600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:227180600-227182200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:227180600-227182600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:227180600-227183000	Strong transcription	Liver	Liver
50	chr1:227180600-227183200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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