Variant report

Variant	rs9352838
Chromosome Location	chr6:81150078-81150079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr6:81149780-81150377	SK-N-SH	brain:	n/a	chr6:81149826-81149835
2	NFIC	chr6:81149416-81150255	SK-N-SH	brain:	n/a	n/a
3	STAT3	chr6:81149884-81150084	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr6:81149835-81150184	MCF10A-Er-Src	breast:	n/a	chr6:81150001-81150011 chr6:81150001-81150011
5	FOS	chr6:81149738-81150521	MCF10A-Er-Src	breast:	n/a	chr6:81150001-81150011 chr6:81150402-81150410 chr6:81150001-81150011
6	FOS	chr6:81149910-81150168	MCF10A-Er-Src	breast:	n/a	chr6:81150001-81150011 chr6:81150001-81150011
7	PBX3	chr6:81149735-81150324	SK-N-SH	brain:	n/a	chr6:81149826-81149835
8	MYC	chr6:81150058-81150258	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr6:81149442-81150511	MCF10A-Er-Src	breast:	n/a	chr6:81150001-81150011 chr6:81150402-81150410 chr6:81150001-81150011
10	TCF12	chr6:81149762-81150401	SK-N-SH	brain:	n/a	chr6:81149841-81149848
11	EP300	chr6:81149855-81150271	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000233967	TF binding region

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs11961045	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1370137	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1436867	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1436868	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1436871	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1698337	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1816564	0.89[CEU][hapmap]
rs1821786	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1836961	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1865917	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2164606	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2164607	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2164608	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2164610	0.98[EUR][1000 genomes]
rs2322770	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917607	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2917608	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3011299	0.84[EUR][1000 genomes]
rs3011300	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3011301	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3011302	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3011304	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4635986	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4637601	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484264	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs484560	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs485088	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs486271	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs487328	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs488098	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505678	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs506825	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs508759	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs512946	0.84[EUR][1000 genomes]
rs514517	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs515347	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs520139	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs522183	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs526071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs528886	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs532709	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs535350	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs536598	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538905	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs540896	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs541446	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs548876	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs553433	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs558478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs559034	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs560068	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs560909	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56112536	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs564757	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs567324	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs568155	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs568253	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs572007	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs574098	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577129	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs577892	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs580525	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs581715	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582966	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs584904	0.89[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs585229	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs586593	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs586605	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs588876	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs593167	0.89[CEU][hapmap]
rs594567	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs596723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs597937	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs597950	0.91[EUR][1000 genomes]
rs598382	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs600549	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs610292	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs612684	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs613998	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs614483	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs615815	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs622089	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs622117	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs622849	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs623286	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs623367	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs624645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs625136	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs630687	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs631481	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs632397	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs634504	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs642613	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs645216	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454158	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs654625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs654955	0.89[CEU][hapmap]
rs655350	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs656381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs661076	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs661119	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66969849	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67220910	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs674031	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs675769	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs681085	0.98[EUR][1000 genomes]
rs687203	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs694288	0.89[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap]
rs73473458	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7752861	0.83[ASN][1000 genomes]
rs7753440	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7757432	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7772873	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs893126	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294175	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9343998	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9352834	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9361616	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9361617	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9443781	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9449007	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034096	chr6:80856135-81150170	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv531333	chr6:81042427-81836484	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1019670	chr6:81086504-81569984	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv915714	chr6:81134888-81366749	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1018028	chr6:81138011-81201697	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9352838	LCA5	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:81142400-81163800	Weak transcription	Ovary	ovary
2	chr6:81143400-81156000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:81143600-81152400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:81143600-81155600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:81146600-81156000	Weak transcription	Pancreas	Pancrea
6	chr6:81147000-81150400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:81147000-81150600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:81147000-81150600	Enhancers	NH-A	brain
9	chr6:81147000-81150800	Enhancers	NHEK	skin
10	chr6:81147400-81150800	Enhancers	HUVEC	blood vessel
11	chr6:81147600-81150200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:81147600-81150800	Enhancers	Hela-S3	cervix
13	chr6:81147800-81150800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:81147800-81151000	Enhancers	HMEC	breast
15	chr6:81148000-81150800	Enhancers	HSMM	muscle
16	chr6:81148400-81150200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr6:81148400-81150200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:81148400-81150600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr6:81148600-81150800	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr6:81148600-81151600	Enhancers	Fetal Intestine Small	intestine
21	chr6:81148600-81151800	Enhancers	Fetal Intestine Large	intestine
22	chr6:81148800-81150800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:81148800-81150800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:81149000-81150400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr6:81149400-81150800	Enhancers	Duodenum Mucosa	Duodenum
26	chr6:81149600-81150200	Enhancers	Brain Germinal Matrix	brain
27	chr6:81149600-81150200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:81149800-81151200	Enhancers	Fetal Brain Female	brain
29	chr6:81150000-81150200	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr6:81150000-81150400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:81150000-81150400	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr6:81150000-81152200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:81150000-81152200	Weak transcription	NHDF-Ad	bronchial

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