Variant report

Variant	rs3734738
Chromosome Location	chr6:57012930-57012931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:57012033-57014304	K562	blood:	n/a	n/a
2	GATA3	chr6:57012470-57013342	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr6:57012486-57013264	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr6:57012472-57013224	SK-N-SH	brain:	n/a	n/a
5	EP300	chr6:57012688-57012950	SK-N-SH_RA	brain:	n/a	n/a
6	PBX3	chr6:57012656-57013192	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:57012321..57014450-chr6:57048955..57051340,2	K562	blood:
2	chr6:56995928..56997999-chr6:57012848..57014485,2	K562	blood:
3	chr6:57011547..57015290-chr6:57018812..57021897,3	MCF-7	breast:
4	chr6:57004320..57006746-chr6:57012025..57013784,2	MCF-7	breast:
5	chr6:57011346..57014118-chr6:57035933..57038689,2	K562	blood:
6	chr6:57011069..57013292-chr6:57014942..57016873,3	K562	blood:

No data

Variant related genes	Relation type
ZNF451	TF binding region
ENSG00000112208	Chromatin interaction
ENSG00000226803	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1157713	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12190416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12190434	0.85[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12192711	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210597	0.96[ASN][1000 genomes]
rs12211611	0.89[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2100305	0.80[ASN][1000 genomes]
rs2273921	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778515	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800019	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs3996929	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3996933	0.80[ASN][1000 genomes]
rs3996937	0.82[ASN][1000 genomes]
rs4715646	0.80[ASN][1000 genomes]
rs6459180	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6913707	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926980	0.93[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];0.85[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6928715	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929783	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6936472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7743855	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7744316	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs7744824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753537	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7753927	0.93[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.80[ASN][1000 genomes]
rs7763570	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180538	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9349843	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9367704	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9367708	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9370564	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9370565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9382680	0.80[YRI][hapmap]
rs9382689	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396259	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952647	0.93[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];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885757	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3734738	RAB23	cis	cerebellum	SCAN
rs3734738	BEND6	cis	lymphoblastoid	seeQTL
rs3734738	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs3734738	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs3734738	BEND6	cis	cerebellum	SCAN
rs3734738	KIAA1586	cis	cerebellum	SCAN
rs3734738	ZNF451	cis	cerebellum	SCAN
rs3734738	BEND6	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56966800-57018000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:56968200-57036400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:56968600-57018400	Weak transcription	Psoas Muscle	Psoas
4	chr6:56985600-57036800	Weak transcription	Pancreas	Pancrea
5	chr6:56991600-57036600	Weak transcription	Small Intestine	intestine
6	chr6:56993000-57017000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:56995800-57036600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:56996000-57036800	Weak transcription	Gastric	stomach
9	chr6:56996200-57036600	Weak transcription	Fetal Brain Male	brain
10	chr6:56996400-57036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:56998800-57027400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:56999800-57036600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:57001200-57013000	Weak transcription	Hela-S3	cervix
14	chr6:57001200-57036600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:57001800-57018600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:57002600-57036600	Weak transcription	A549	lung
17	chr6:57005600-57013600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr6:57005600-57021600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:57005600-57023400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:57005600-57023800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:57005800-57022400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:57006200-57028600	Strong transcription	Liver	Liver
23	chr6:57006600-57013800	Strong transcription	Adipose Nuclei	Adipose
24	chr6:57006600-57021600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:57006600-57036600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:57007400-57017000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:57007600-57014200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:57007600-57018400	Weak transcription	Brain Angular Gyrus	brain
29	chr6:57008000-57017800	Weak transcription	Brain Substantia Nigra	brain
30	chr6:57008400-57022000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:57008600-57018600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:57009000-57017200	Weak transcription	Fetal Brain Female	brain
33	chr6:57009400-57013600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:57009600-57016000	Weak transcription	Fetal Stomach	stomach
35	chr6:57009800-57018000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:57009800-57018000	Weak transcription	Fetal Intestine Small	intestine
37	chr6:57010000-57013400	Strong transcription	Placenta	Placenta
38	chr6:57010000-57021400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:57010600-57014400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:57010800-57024600	Strong transcription	Primary B cells from cord blood	blood
41	chr6:57011200-57013400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:57011400-57013400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:57011400-57013600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr6:57011400-57014000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:57011400-57014200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:57011400-57020000	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:57011400-57020000	Strong transcription	HepG2	liver
48	chr6:57011400-57021400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr6:57011400-57036600	Weak transcription	Stomach Mucosa	stomach
50	chr6:57011600-57013600	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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