Variant report

Variant	rs2695783
Chromosome Location	chr12:56588453-56588454
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56550919..56553692-chr12:56586554..56588922,4	MCF-7	breast:
2	chr12:56587021..56588859-chr12:56589335..56591396,2	MCF-7	breast:
3	chr12:56582670..56585645-chr12:56588160..56590728,3	MCF-7	breast:
4	chr12:56579883..56589030-chr12:56613342..56620091,21	MCF-7	breast:
5	chr12:56586857..56589581-chr12:56659506..56661995,3	K562	blood:
6	chr12:56583715..56585705-chr12:56588416..56589988,2	K562	blood:
7	chr12:56579404..56590957-chr12:56614094..56620955,25	MCF-7	breast:
8	chr12:56585829..56588908-chr12:56597306..56601044,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257809	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000181852	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10129008	1.00[EUR][1000 genomes]
rs10747763	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10876878	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171753	1.00[TSI][hapmap]
rs11171754	1.00[EUR][1000 genomes]
rs11171755	1.00[EUR][1000 genomes]
rs11171772	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11171777	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11171823	1.00[TSI][hapmap]
rs11834728	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12229022	0.95[ASN][1000 genomes]
rs12306670	1.00[TSI][hapmap]
rs12309480	1.00[EUR][1000 genomes]
rs12311878	1.00[TSI][hapmap]
rs12320265	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274502	1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274503	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1405859	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689518	1.00[CHD][hapmap]
rs17118333	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2271188	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2271190	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2271192	1.00[JPT][hapmap]
rs2277340	1.00[CHD][hapmap]
rs2463365	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2629453	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2695784	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28676339	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2930787	0.95[AMR][1000 genomes]
rs2930788	0.94[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950573	1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759096	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3802996	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3809130	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4759218	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs55887836	1.00[EUR][1000 genomes]
rs56851901	0.83[ASN][1000 genomes]
rs57280585	0.83[ASN][1000 genomes]
rs57822276	0.83[ASN][1000 genomes]
rs58009483	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58476735	0.83[ASN][1000 genomes]
rs58548156	0.83[ASN][1000 genomes]
rs58663297	0.83[ASN][1000 genomes]
rs59053322	1.00[ASN][1000 genomes]
rs59078852	1.00[ASN][1000 genomes]
rs59420211	1.00[EUR][1000 genomes]
rs59966703	1.00[ASN][1000 genomes]
rs60396934	0.83[ASN][1000 genomes]
rs61939011	1.00[ASN][1000 genomes]
rs6581091	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs703823	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136420	1.00[TSI][hapmap]
rs7311008	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs73340401	1.00[EUR][1000 genomes]
rs74092003	1.00[EUR][1000 genomes]
rs7489249	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772925	1.00[TSI][hapmap]
rs772926	1.00[TSI][hapmap]
rs773654	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs773655	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs773658	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773659	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773660	0.90[ASN][1000 genomes]
rs773661	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773663	1.00[TSI][hapmap]
rs7956599	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7956926	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7962107	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7967464	1.00[ASN][1000 genomes]
rs7975405	1.00[ASN][1000 genomes]
rs7975486	1.00[TSI][hapmap]

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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv973989	chr12:56582243-56602996	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2695783	HLA-DPB1	trans	lymphoblastoid	seeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56584200-56598000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:56584600-56598000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:56584600-56598000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:56584600-56598200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:56584600-56598400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:56584600-56600000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:56584800-56590000	Weak transcription	Placenta	Placenta
8	chr12:56584800-56590200	Weak transcription	NH-A	brain
9	chr12:56584800-56590800	Weak transcription	Fetal Heart	heart
10	chr12:56584800-56591400	Weak transcription	NHLF	lung
11	chr12:56584800-56596400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:56584800-56597800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:56584800-56597800	Weak transcription	Fetal Thymus	thymus
14	chr12:56584800-56598000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:56584800-56598000	Weak transcription	Primary B cells from cord blood	blood
16	chr12:56584800-56598000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:56584800-56598000	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:56584800-56598000	Weak transcription	Fetal Stomach	stomach
19	chr12:56584800-56598200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:56584800-56598400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr12:56584800-56598600	Weak transcription	Ovary	ovary
22	chr12:56584800-56598800	Weak transcription	HMEC	breast
23	chr12:56584800-56599000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:56584800-56599400	Weak transcription	Pancreas	Pancrea
25	chr12:56584800-56599600	Weak transcription	Colonic Mucosa	Colon
26	chr12:56585000-56590600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:56585000-56592000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:56585000-56592600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:56585000-56592600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:56585000-56597800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr12:56585000-56597800	Weak transcription	Primary T cells from cord blood	blood
32	chr12:56585000-56597800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:56585000-56598000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:56585000-56598000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:56585000-56598000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:56585000-56598000	Weak transcription	Fetal Brain Female	brain
37	chr12:56585000-56598000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:56585000-56598200	Weak transcription	A549	lung
39	chr12:56585000-56598400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr12:56585000-56598400	Weak transcription	NHDF-Ad	bronchial
41	chr12:56585000-56614800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr12:56585200-56590800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:56585200-56592800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:56585200-56598000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:56585400-56590600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:56585800-56590600	Weak transcription	Adipose Nuclei	Adipose
47	chr12:56585800-56598200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr12:56587200-56590000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:56587200-56590600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:56587200-56598000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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