Variant report

Variant	rs9343918
Chromosome Location	chr6:80249304-80249305
allele	A/T
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	MXI1	chr6:80245777-80249441	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr6:80245862-80249600	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr6:80246317-80249494	MCF10A-Er-Src	breast:	n/a	n/a
4	KAP1	chr6:80249140-80249645	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:79786363..79788558-chr6:80246704..80249654,3	K562	blood:
2	chr6:80247904..80250067-chr6:80253206..80255779,2	MCF-7	breast:
3	chr6:79784764..79788097-chr6:80246158..80249987,4	MCF-7	breast:
4	chr6:79786974..79789353-chr6:80246033..80249654,3	K562	blood:
5	chr6:80245821..80247636-chr6:80249028..80251095,2	K562	blood:

Variant related genes	Relation type
LCA5	TF binding region
ENSG00000146247	Chromatin interaction
ENSG00000135338	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10943650	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10943651	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13206818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1351959	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1354452	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs1485374	0.80[JPT][hapmap]
rs2009837	0.81[AFR][1000 genomes]
rs2047896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2655662	0.87[CHB][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2655700	0.82[CHB][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs2655701	0.80[ASN][1000 genomes]
rs2812689	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2812692	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs3747766	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3967183	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4055084	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4706789	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs66572100	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6915859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6930436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72624517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7754849	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9294148	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9341781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9341782	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9343919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9343920	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9343921	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9352736	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9352737	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9352738	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9352739	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9352743	0.83[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9352744	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9352747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9359379	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9359382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9359383	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9359384	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9361537	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9361538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9361539	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs958114	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv886303	chr6:80147225-80252423	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv463906	chr6:80240951-80313297	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv604052	chr6:80240951-80313297	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80243000-80249400	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr6:80245400-80249400	Active TSS	Right Atrium	heart
3	chr6:80245600-80249400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:80245800-80249400	Active TSS	K562	blood
5	chr6:80245800-80249600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:80246000-80249400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr6:80246000-80249600	Active TSS	Brain Angular Gyrus	brain
8	chr6:80246200-80249400	Active TSS	Fetal Brain Female	brain
9	chr6:80246400-80249400	Active TSS	Brain Anterior Caudate	brain
10	chr6:80246400-80249400	Active TSS	Brain Cingulate Gyrus	brain
11	chr6:80247600-80267800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:80247800-80253800	Weak transcription	Small Intestine	intestine
13	chr6:80247800-80256800	Weak transcription	Lung	lung
14	chr6:80247800-80257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:80247800-80257000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:80247800-80257600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:80248000-80262000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:80248200-80253600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:80248600-80249600	Enhancers	Colon Smooth Muscle	Colon
20	chr6:80248600-80250600	Weak transcription	Fetal Stomach	stomach
21	chr6:80248600-80251200	Weak transcription	Placenta	Placenta
22	chr6:80248600-80251600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:80248600-80251800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:80248600-80252000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:80248600-80254000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:80248600-80254000	Weak transcription	Primary T cells from cord blood	blood
27	chr6:80248600-80254000	Weak transcription	Hela-S3	cervix
28	chr6:80248600-80262800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:80248600-80262800	Weak transcription	Liver	Liver
30	chr6:80248800-80249400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:80248800-80249400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr6:80248800-80249400	Active TSS	Brain Substantia Nigra	brain
33	chr6:80248800-80249400	Enhancers	Fetal Heart	heart
34	chr6:80248800-80249600	Enhancers	Fetal Lung	lung
35	chr6:80248800-80249600	Enhancers	HepG2	liver
36	chr6:80248800-80250600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:80248800-80250600	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:80248800-80251200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:80248800-80251200	Weak transcription	Fetal Intestine Large	intestine
40	chr6:80248800-80251200	Weak transcription	Left Ventricle	heart
41	chr6:80248800-80251200	Weak transcription	HSMM	muscle
42	chr6:80248800-80251600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:80248800-80252600	Weak transcription	GM12878-XiMat	blood
44	chr6:80248800-80253000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:80248800-80253200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:80248800-80253200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:80248800-80253200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:80248800-80253200	Weak transcription	NHLF	lung
49	chr6:80248800-80253400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:80248800-80253600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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