Variant report

Variant	rs3858627
Chromosome Location	chr12:51745478-51745479
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51159003..51159746-chr12:51745461..51746336,2	K562	blood:
2	chr12:51662264..51665283-chr12:51745297..51747465,3	K562	blood:
3	chr12:51734941..51739498-chr12:51744423..51748065,5	K562	blood:
4	chr12:51744372..51748268-chr12:51756905..51759729,4	K562	blood:
5	chr12:51714696..51717509-chr12:51745471..51747033,2	MCF-7	breast:
6	chr12:51441280..51444117-chr12:51744506..51748458,5	MCF-7	breast:
7	chr12:51441102..51443608-chr12:51745304..51746823,2	K562	blood:
8	chr12:51631532..51634032-chr12:51744589..51747276,3	MCF-7	breast:
9	chr12:51745453..51745976-chr5:73263142..73263663,3	MCF-7	breast:
10	chr12:51745450..51746290-chr12:51814696..51815264,2	MCF-7	breast:
11	chr12:50468698..50469628-chr12:51745397..51745900,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000170545	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000183283	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10516	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876162	0.84[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs11169795	0.89[ASW][hapmap];0.81[CEU][hapmap];0.84[TSI][hapmap]
rs11169805	0.84[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs11616158	0.83[EUR][1000 genomes]
rs12310910	0.94[ASN][1000 genomes]
rs12582273	0.84[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.99[ASN][1000 genomes]
rs12829179	0.82[EUR][1000 genomes]
rs12831721	0.87[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs17860300	0.83[EUR][1000 genomes]
rs17860301	0.83[EUR][1000 genomes]
rs17860343	0.83[EUR][1000 genomes]
rs3858624	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133606	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138439	0.84[CEU][hapmap];0.89[TSI][hapmap]
rs7299306	0.86[EUR][1000 genomes]
rs7299453	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7959814	0.84[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs7964134	0.86[EUR][1000 genomes]
rs9651999	0.86[EUR][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	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	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
3	esv3325259	chr12:51744741-51746212	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3858627	ELA1	cis	multi-tissue	Pritchard
rs3858627	LOC57228	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51731800-51750600	Weak transcription	Spleen	Spleen
2	chr12:51735400-51745800	Weak transcription	Fetal Intestine Small	intestine
3	chr12:51735400-51746800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:51735400-51747400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:51735400-51747400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:51735400-51747400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr12:51735400-51747600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr12:51735400-51747800	Weak transcription	NHLF	lung
9	chr12:51735400-51750200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:51735400-51750600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:51735400-51750600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:51735400-51756000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:51735600-51746800	Weak transcription	Primary T cells from cord blood	blood
14	chr12:51735600-51750600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:51735600-51761400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:51735800-51747400	Weak transcription	Dnd41	blood
17	chr12:51736400-51765400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:51739400-51748400	Weak transcription	Gastric	stomach
19	chr12:51739400-51754200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:51739600-51750600	Weak transcription	GM12878-XiMat	blood
21	chr12:51740000-51747400	Weak transcription	NHEK	skin
22	chr12:51740200-51745800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:51740200-51746800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:51740400-51747400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:51740400-51747400	Weak transcription	Thymus	Thymus
26	chr12:51740400-51747800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:51740600-51747600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:51740600-51751000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:51740800-51753200	Weak transcription	NHDF-Ad	bronchial
30	chr12:51741000-51745600	Weak transcription	Fetal Thymus	thymus
31	chr12:51741000-51747800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr12:51742200-51745800	Weak transcription	K562	blood
33	chr12:51742400-51746000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr12:51742400-51749600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:51743200-51750600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:51743400-51745600	Weak transcription	Osteobl	bone
37	chr12:51743400-51746200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:51743400-51746800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:51743400-51751600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:51744000-51746400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:51744000-51748000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr12:51744200-51761400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr12:51744800-51746400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:51745200-51745800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr12:51745200-51746200	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr12:51745200-51746200	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr12:51745400-51745800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:51745400-51746200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr12:51745400-51746200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr12:51745400-51746200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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