Variant report

Variant	rs6734445
Chromosome Location	chr2:54797798-54797799
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54782556..54791633-chr2:54796824..54803982,19	MCF-7	breast:
2	chr2:54796760..54799671-chr2:54800450..54802770,2	K562	blood:
3	chr2:54795805..54798083-chr2:54801150..54802782,2	MCF-7	breast:
4	chr2:54749225..54752072-chr2:54796311..54798001,2	K562	blood:
5	chr2:54783962..54788714-chr2:54796833..54801765,9	K562	blood:
6	chr2:54797362..54799747-chr2:54810321..54813282,3	K562	blood:
7	chr2:54797516..54799490-chr2:54803547..54805303,2	K562	blood:
8	chr2:54796611..54799496-chr2:54810522..54814074,3	MCF-7	breast:
9	chr2:54781728..54792106-chr2:54796721..54808716,28	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10166844	0.98[ASN][1000 genomes]
rs10169439	0.89[CEU][hapmap]
rs10169954	0.93[ASN][1000 genomes]
rs10169975	0.91[ASN][1000 genomes]
rs10170066	0.95[ASN][1000 genomes]
rs10170355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10176359	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs10176445	1.00[CHB][hapmap]
rs10182538	0.95[ASN][1000 genomes]
rs10182836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10183043	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10183867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10184128	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.97[ASN][1000 genomes]
rs10187338	0.95[ASN][1000 genomes]
rs10188185	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs10188545	0.90[ASN][1000 genomes]
rs10193692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10205410	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs10206143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10208225	0.95[ASN][1000 genomes]
rs10210502	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10528	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[EUR][1000 genomes]
rs1137645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11555856	0.87[EUR][1000 genomes]
rs11892236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs11892443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11896957	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11898032	0.92[ASN][1000 genomes]
rs11898033	0.92[ASN][1000 genomes]
rs11902987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11904679	0.85[CEU][hapmap];0.89[CHB][hapmap];0.81[EUR][1000 genomes]
rs12713262	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713263	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713264	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[LWK][hapmap];0.95[ASN][1000 genomes]
rs12713265	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[ASN][1000 genomes]
rs12713266	0.95[ASN][1000 genomes]
rs12713267	0.92[ASN][1000 genomes]
rs12713268	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12713269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12713270	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12713271	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12713273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713274	0.86[ASN][1000 genomes]
rs12987967	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13021606	0.85[EUR][1000 genomes]
rs13021615	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[EUR][1000 genomes]
rs13036147	0.80[EUR][1000 genomes]
rs13386146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13391522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13391803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13399656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13403284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13407214	0.97[ASN][1000 genomes]
rs13428703	0.85[CEU][hapmap]
rs13432302	0.95[ASN][1000 genomes]
rs17039558	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[GIH][hapmap];0.88[EUR][1000 genomes]
rs17045939	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.80[EUR][1000 genomes]
rs17046061	0.84[EUR][1000 genomes]
rs17046067	0.84[EUR][1000 genomes]
rs17046077	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs17046097	0.86[JPT][hapmap]
rs17046108	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs17046257	1.00[CHB][hapmap]
rs2048370	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2229503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2271329	0.85[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs28581481	0.93[ASN][1000 genomes]
rs3287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34077590	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34094680	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34263579	0.84[EUR][1000 genomes]
rs34308676	0.88[EUR][1000 genomes]
rs34311770	0.84[EUR][1000 genomes]
rs34429083	0.81[EUR][1000 genomes]
rs34978408	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs354232	0.89[CHB][hapmap]
rs35619551	0.83[EUR][1000 genomes]
rs36018286	0.82[EUR][1000 genomes]
rs3739109	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3796017	0.95[ASN][1000 genomes]
rs3796018	0.95[ASN][1000 genomes]
rs3796019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3796022	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[GIH][hapmap];0.82[EUR][1000 genomes]
rs4261758	0.92[CEU][hapmap];0.89[CHB][hapmap];0.85[EUR][1000 genomes]
rs4319969	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs4346422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4347868	0.89[ASN][1000 genomes]
rs4358162	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4374410	0.93[ASN][1000 genomes]
rs4455200	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4519566	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45487791	0.82[EUR][1000 genomes]
rs4577321	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4616509	0.95[ASN][1000 genomes]
rs4641979	0.95[ASN][1000 genomes]
rs57281248	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58419243	0.84[EUR][1000 genomes]
rs61126015	0.86[EUR][1000 genomes]
rs6545430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs6545440	0.85[CEU][hapmap]
rs66693131	0.82[EUR][1000 genomes]
rs6706263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs67079536	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6708082	0.85[CEU][hapmap]
rs6721612	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6724136	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67244067	0.81[EUR][1000 genomes]
rs6730876	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6734536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6739140	0.92[ASN][1000 genomes]
rs6741053	0.81[EUR][1000 genomes]
rs6749802	0.92[ASN][1000 genomes]
rs6752720	0.85[CEU][hapmap]
rs6753004	0.85[CEU][hapmap]
rs72806653	0.80[EUR][1000 genomes]
rs7340302	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.97[ASN][1000 genomes]
rs7424459	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7556752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7564719	0.90[ASN][1000 genomes]
rs7569127	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs7582640	0.85[CEU][hapmap]
rs7584223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7586066	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7586311	0.95[ASN][1000 genomes]
rs7599241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7602992	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7608414	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs9677089	0.85[ASN][1000 genomes]

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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6734445	C2orf63	cis	cerebellum	SCAN
rs6734445	EML6	cis	Thyroid	GTEx
rs6734445	VRK2	cis	cerebellum	SCAN
rs6734445	RPL23AP32	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54789800-54801400	Enhancers	Liver	Liver
2	chr2:54791200-54801200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr2:54793000-54799800	Enhancers	Stomach Mucosa	stomach
4	chr2:54794400-54804200	Weak transcription	Ovary	ovary
5	chr2:54795000-54799400	Enhancers	Fetal Heart	heart
6	chr2:54795200-54799000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:54795200-54799800	Enhancers	Fetal Intestine Large	intestine
8	chr2:54795200-54802200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:54795400-54799200	Enhancers	HUVEC	blood vessel
10	chr2:54795400-54801400	Enhancers	Fetal Thymus	thymus
11	chr2:54795600-54799400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr2:54795600-54802400	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr2:54795800-54797800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:54795800-54798400	Enhancers	NH-A	brain
15	chr2:54795800-54798800	Enhancers	Right Ventricle	heart
16	chr2:54795800-54799200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:54795800-54799400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:54795800-54799400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr2:54795800-54799400	Flanking Active TSS	A549	lung
20	chr2:54795800-54800000	Enhancers	NHLF	lung
21	chr2:54795800-54801200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:54795800-54801800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr2:54795800-54801800	Enhancers	Fetal Kidney	kidney
24	chr2:54795800-54802400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:54795800-54803000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr2:54795800-54803200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr2:54795800-54803400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr2:54795800-54807000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr2:54795800-54807600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr2:54796000-54797800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:54796000-54797800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr2:54796000-54798200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:54796000-54798200	Enhancers	Osteobl	bone
34	chr2:54796000-54799400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr2:54796000-54799400	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr2:54796000-54801200	Enhancers	Thymus	Thymus
37	chr2:54796000-54801600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:54796000-54801600	Enhancers	Brain Substantia Nigra	brain
39	chr2:54796000-54801800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:54796000-54802000	Enhancers	Brain Cingulate Gyrus	brain
41	chr2:54796000-54802000	Enhancers	Fetal Lung	lung
42	chr2:54796000-54802200	Enhancers	HSMMtube	muscle
43	chr2:54796000-54802400	Enhancers	Brain Hippocampus Middle	brain
44	chr2:54796000-54802600	Enhancers	HMEC	breast
45	chr2:54796000-54802800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr2:54796000-54804400	Enhancers	Adipose Nuclei	Adipose
47	chr2:54796000-54807600	Enhancers	Brain Angular Gyrus	brain
48	chr2:54796200-54798200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:54796200-54798200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:54796200-54798400	Enhancers	H1 Cell Line	embryonic stem cell

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