Variant report

Variant	rs3847862
Chromosome Location	chr12:51732500-51732501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51476882..51478669-chr12:51732135..51734824,2	K562	blood:
2	chr12:51661063..51664468-chr12:51732483..51736872,6	MCF-7	breast:
3	chr12:51661930..51666177-chr12:51732145..51735624,5	MCF-7	breast:
4	chr12:51632808..51635025-chr12:51730960..51733837,2	MCF-7	breast:
5	chr12:51732471..51736842-chr12:51740584..51742945,3	MCF-7	breast:
6	chr12:51474705..51477188-chr12:51731432..51735357,3	K562	blood:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000170545	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10783431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169806	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169813	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11612245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305814	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580599	0.96[CEU][hapmap];0.98[TSI][hapmap]
rs12816187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145127	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4335588	0.82[EUR][1000 genomes]
rs56869579	0.82[EUR][1000 genomes]
rs7301933	0.81[EUR][1000 genomes]
rs934089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9652000	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51720800-51735000	Weak transcription	Esophagus	oesophagus
2	chr12:51721200-51735000	Weak transcription	NHDF-Ad	bronchial
3	chr12:51722600-51735000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:51724200-51735000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:51724400-51734800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:51724400-51739200	Weak transcription	Thymus	Thymus
7	chr12:51725400-51735000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:51726000-51734800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:51728200-51735000	Weak transcription	Colonic Mucosa	Colon
10	chr12:51728800-51735000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:51730600-51734800	Weak transcription	Hela-S3	cervix
12	chr12:51730800-51734800	Weak transcription	A549	lung
13	chr12:51730800-51734800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr12:51730800-51735000	Weak transcription	GM12878-XiMat	blood
15	chr12:51731000-51733800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:51731000-51734800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr12:51731000-51734800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:51731000-51735000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr12:51731000-51735000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:51731200-51734800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:51731200-51735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:51731200-51735000	Weak transcription	K562	blood
23	chr12:51731800-51750600	Weak transcription	Spleen	Spleen
24	chr12:51732400-51735000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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