Variant report

Variant	rs4699012
Chromosome Location	chr4:103249884-103249885
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	chr4:103242499..103244957-chr4:103246433..103250034,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10461136	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1117520	0.81[CEU][hapmap]
rs11730379	0.80[EUR][1000 genomes]
rs11931217	0.87[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs12499248	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12510124	0.87[GIH][hapmap]
rs1381893	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1462943	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1462950	0.82[CEU][hapmap]
rs1462952	0.83[CEU][hapmap]
rs2054393	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233820	0.81[JPT][hapmap]
rs34663993	0.86[ASN][1000 genomes]
rs34835832	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4557261	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4699026	0.85[GIH][hapmap]
rs56202729	0.84[ASN][1000 genomes]
rs62329487	0.84[ASN][1000 genomes]
rs6533014	0.83[GIH][hapmap]
rs6814302	0.95[GIH][hapmap]
rs6844796	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6848517	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7436937	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs985989	0.94[CHB][hapmap];0.86[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428447	chr4:103103730-103262107	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4699012	METAP1	cis	parietal	SCAN
rs4699012	GSTCD	cis	parietal	SCAN
rs4699012	EFNA1	trans	parietal	SCAN
rs4699012	ADH1C	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103182000-103255400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr4:103210400-103256800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:103224000-103263600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:103237400-103264000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:103239000-103256800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:103241200-103263600	Weak transcription	Liver	Liver
7	chr4:103241200-103263600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:103242600-103263400	Weak transcription	Lung	lung
9	chr4:103242800-103259600	Weak transcription	K562	blood
10	chr4:103243200-103256400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:103243400-103257000	Weak transcription	Dnd41	blood
12	chr4:103243400-103258600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:103243800-103255000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:103243800-103256800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:103244000-103262000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:103244000-103262000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:103244200-103255200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:103244600-103260200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:103245000-103250200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:103245000-103257200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:103245000-103257400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:103245200-103253400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:103246000-103253400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:103246200-103250400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:103246600-103250200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:103249800-103250000	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr4:103249800-103260200	Weak transcription	Hela-S3	cervix

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