Variant report

Variant	rs6743051
Chromosome Location	chr2:85844161-85844162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr2:85844094-85844222	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:85842888-85844262	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:85844082-85844195	K562	blood:	n/a	n/a
4	MXI1	chr2:85842895-85844494	SK-N-SH	brain:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85581050..85582551-chr2:85842255..85845112,2	K562	blood:
2	chr2:85764278..85767937-chr2:85842194..85845131,5	K562	blood:
3	chr2:85554801..85556928-chr2:85841826..85844560,3	K562	blood:
4	chr2:85781220..85783069-chr2:85843388..85844916,2	K562	blood:
5	chr2:85635586..85637613-chr2:85842504..85845075,3	K562	blood:
6	chr2:85635586..85637613-chr2:85842504..85845075,2	K562	blood:
7	chr2:85788090..85790276-chr2:85843561..85845118,2	MCF-7	breast:
8	chr2:85842186..85844558-chr2:85848833..85852052,4	MCF-7	breast:
9	chr2:85643378..85649324-chr2:85837656..85846268,13	K562	blood:
10	chr2:85843668..85846155-chr2:85873712..85875866,3	K562	blood:
11	chr2:85765143..85767907-chr2:85841259..85844982,5	MCF-7	breast:
12	chr2:85625848..85628085-chr2:85842277..85844956,2	MCF-7	breast:
13	chr2:85579163..85582551-chr2:85842255..85845885,4	K562	blood:
14	chr2:85787265..85788881-chr2:85843374..85845144,2	K562	blood:
15	chr2:85644680..85648320-chr2:85841692..85845956,4	K562	blood:
16	chr2:85764765..85769369-chr2:85840508..85847982,10	K562	blood:
17	chr2:85555196..85556928-chr2:85841826..85844560,2	K562	blood:
18	chr2:85843641..85846530-chr2:85864752..85867588,2	K562	blood:
19	chr2:85837207..85840832-chr2:85841070..85844212,15	K562	blood:
20	chr2:85843601..85846155-chr2:85873808..85876002,2	K562	blood:

No data

Variant related genes	Relation type
C2orf68	TF binding region
ENSG00000168887	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000118640	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10180770	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10182351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10190428	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10191726	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10302	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1044158	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs1124836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13383605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13414982	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs13418207	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs14242	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1446669	0.84[JPT][hapmap]
rs1562322	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1992151	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2028898	0.84[JPT][hapmap]
rs2043675	0.84[JPT][hapmap]
rs2118176	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2232747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232748	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2232750	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592551	0.84[JPT][hapmap]
rs3024831	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs3198089	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3755009	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3755010	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755011	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821020	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3827550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6547629	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6733550	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs699664	0.84[JPT][hapmap]
rs762684	0.84[JPT][hapmap]

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	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6743051	hmm28069	cis	multi-tissue	Pritchard
rs6743051	VAMP8	cis	lymphoblastoid	seeQTL
rs6743051	LOC388969	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85842400-85844400	Active TSS	GM12878-XiMat	blood
2	chr2:85842600-85844200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr2:85842600-85844400	Active TSS	Brain Anterior Caudate	brain
4	chr2:85842600-85845000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr2:85842800-85844200	Active TSS	H1 Cell Line	embryonic stem cell
6	chr2:85842800-85844200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:85842800-85844200	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr2:85842800-85844200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:85842800-85844200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:85842800-85844200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:85842800-85844200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:85842800-85844200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:85842800-85844200	Active TSS	Esophagus	oesophagus
14	chr2:85842800-85844200	Active TSS	Fetal Brain Female	brain
15	chr2:85842800-85844200	Active TSS	Fetal Intestine Small	intestine
16	chr2:85842800-85844200	Active TSS	Fetal Kidney	kidney
17	chr2:85842800-85844200	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr2:85842800-85844200	Active TSS	Osteobl	bone
19	chr2:85842800-85844400	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr2:85842800-85844400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr2:85842800-85844400	Active TSS	Brain Angular Gyrus	brain
22	chr2:85842800-85844600	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr2:85842800-85844600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:85842800-85844800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:85843000-85844200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:85843000-85844200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:85843000-85844200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:85843000-85844200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:85843000-85844200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:85843000-85844200	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr2:85843000-85844200	Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr2:85843000-85844200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:85843000-85844200	Active TSS	Muscle Satellite Cultured Cells	--
34	chr2:85843000-85844200	Active TSS	Brain Hippocampus Middle	brain
35	chr2:85843000-85844200	Active TSS	Colon Smooth Muscle	Colon
36	chr2:85843000-85844200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr2:85843000-85844200	Active TSS	Left Ventricle	heart
38	chr2:85843000-85844200	Active TSS	Ovary	ovary
39	chr2:85843000-85844200	Active TSS	Right Ventricle	heart
40	chr2:85843000-85844200	Active TSS	Small Intestine	intestine
41	chr2:85843000-85844200	Active TSS	HMEC	breast
42	chr2:85843000-85844200	Active TSS	HSMM	muscle
43	chr2:85843000-85844200	Active TSS	HUVEC	blood vessel
44	chr2:85843000-85844200	Active TSS	NH-A	brain
45	chr2:85843000-85844200	Active TSS	NHDF-Ad	bronchial
46	chr2:85843000-85844200	Active TSS	NHEK	skin
47	chr2:85843000-85844200	Active TSS	NHLF	lung
48	chr2:85843000-85844400	Active TSS	H9 Cell Line	embryonic stem cell
49	chr2:85843000-85844400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:85843000-85844400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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