Variant report

Variant	rs16890835
Chromosome Location	chr6:80248991-80248992
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	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	RFX5	chr6:80245421-80249050	SK-N-SH	brain:	n/a	chr6:80248388-80248397 chr6:80247194-80247203
4	POLR2A	chr6:80246317-80249494	MCF10A-Er-Src	breast:	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:

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

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10498921	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158770	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158771	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11965020	0.92[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966497	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385536	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1385537	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1485370	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1485372	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504368	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16890774	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890850	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890862	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890875	0.84[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17335231	0.84[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17727505	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2575204	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2575208	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629472	0.82[EUR][1000 genomes]
rs2629473	0.81[EUR][1000 genomes]
rs2655666	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655677	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655679	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2655680	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655703	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2803188	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803189	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803197	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269343	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55830218	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55989614	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56087572	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56745436	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61152095	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411332	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411348	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413360	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413362	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62413363	0.83[EUR][1000 genomes]
rs62413366	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413368	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413370	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413371	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62413372	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413377	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413380	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413382	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413385	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413387	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413388	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413389	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413390	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413391	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413395	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413396	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413399	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62413401	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62413416	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6454124	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454125	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907133	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917186	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920635	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921102	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925212	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926534	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934060	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73747413	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73750727	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7745158	0.84[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745429	0.84[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749776	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760677	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761245	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763266	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763268	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768651	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768724	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769778	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7772722	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775232	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992872	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:85 , 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	chr6:80245000-80249200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:80245400-80249400	Active TSS	Right Atrium	heart
4	chr6:80245600-80249400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:80245800-80249400	Active TSS	K562	blood
6	chr6:80245800-80249600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:80246000-80249000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:80246000-80249400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:80246000-80249600	Active TSS	Brain Angular Gyrus	brain
10	chr6:80246200-80249200	Active TSS	Brain Hippocampus Middle	brain
11	chr6:80246200-80249400	Active TSS	Fetal Brain Female	brain
12	chr6:80246400-80249000	Active TSS	HMEC	breast
13	chr6:80246400-80249400	Active TSS	Brain Anterior Caudate	brain
14	chr6:80246400-80249400	Active TSS	Brain Cingulate Gyrus	brain
15	chr6:80247600-80267800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:80247800-80253800	Weak transcription	Small Intestine	intestine
17	chr6:80247800-80256800	Weak transcription	Lung	lung
18	chr6:80247800-80257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:80247800-80257000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:80247800-80257600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:80248000-80249000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:80248000-80262000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:80248200-80249000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr6:80248200-80253600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:80248400-80249000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:80248600-80249000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:80248600-80249600	Enhancers	Colon Smooth Muscle	Colon
28	chr6:80248600-80250600	Weak transcription	Fetal Stomach	stomach
29	chr6:80248600-80251200	Weak transcription	Placenta	Placenta
30	chr6:80248600-80251600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:80248600-80251800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr6:80248600-80252000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:80248600-80254000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:80248600-80254000	Weak transcription	Primary T cells from cord blood	blood
35	chr6:80248600-80254000	Weak transcription	Hela-S3	cervix
36	chr6:80248600-80262800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:80248600-80262800	Weak transcription	Liver	Liver
38	chr6:80248800-80249000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr6:80248800-80249000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:80248800-80249000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:80248800-80249000	Active TSS	NH-A	brain
42	chr6:80248800-80249000	Active TSS	Osteobl	bone
43	chr6:80248800-80249200	Enhancers	HUVEC	blood vessel
44	chr6:80248800-80249400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:80248800-80249400	Enhancers	Muscle Satellite Cultured Cells	--
46	chr6:80248800-80249400	Active TSS	Brain Substantia Nigra	brain
47	chr6:80248800-80249400	Enhancers	Fetal Heart	heart
48	chr6:80248800-80249600	Enhancers	Fetal Lung	lung
49	chr6:80248800-80249600	Enhancers	HepG2	liver
50	chr6:80248800-80250600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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