Variant report

Variant	rs62559493
Chromosome Location	chr9:22238595-22238596
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:33)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:22082310..22089949-chr9:22236353..22239754,11	MCF-7	breast:
2	chr9:22051314..22055495-chr9:22237121..22240202,3	MCF-7	breast:
3	chr9:21800909..21803177-chr9:22237064..22239100,3	MCF-7	breast:
4	chr9:21999310..22001355-chr9:22237722..22240427,2	MCF-7	breast:
5	chr9:22236750..22240828-chr9:22241723..22245901,7	MCF-7	breast:
6	chr9:21989791..21997438-chr9:22235038..22242897,11	MCF-7	breast:
7	chr9:22115148..22116731-chr9:22237636..22239913,2	MCF-7	breast:
8	chr9:22208635..22217579-chr9:22235952..22243529,17	MCF-7	breast:
9	chr9:22237736..22240719-chr9:22245980..22248621,2	MCF-7	breast:
10	chr9:21811209..21815369-chr9:22236301..22242853,10	MCF-7	breast:
11	chr9:21992318..21994431-chr9:22237901..22239689,2	MCF-7	breast:
12	chr9:22157848..22160460-chr9:22237731..22240961,3	MCF-7	breast:
13	chr9:22134724..22142146-chr9:22236106..22241744,12	MCF-7	breast:
14	chr9:22096125..22098594-chr9:22238044..22240810,3	MCF-7	breast:
15	chr9:22123951..22126513-chr9:22237605..22240050,3	MCF-7	breast:
16	chr9:22132234..22134475-chr9:22237338..22238952,2	MCF-7	breast:
17	chr9:22108454..22110071-chr9:22237299..22239893,2	MCF-7	breast:
18	chr9:22117114..22119217-chr9:22236717..22238636,2	MCF-7	breast:
19	chr9:22133587..22139389-chr9:22236165..22240719,9	MCF-7	breast:
20	chr9:22006917..22010967-chr9:22237513..22242340,6	MCF-7	breast:
21	chr2:32580250..32582007-chr9:22237411..22239616,2	MCF-7	breast:
22	chr9:22083985..22087437-chr9:22237738..22239809,4	MCF-7	breast:
23	chr9:21812198..21814272-chr9:22238203..22240470,3	MCF-7	breast:
24	chr9:22218358..22220898-chr9:22236152..22238994,2	MCF-7	breast:
25	chr9:22208810..22215725-chr9:22233777..22241391,18	MCF-7	breast:
26	chr9:22001061..22004369-chr9:22238079..22242030,5	MCF-7	breast:
27	chr9:22119464..22121250-chr9:22237371..22239019,2	MCF-7	breast:
28	chr9:22100911..22107878-chr9:22236967..22244514,15	MCF-7	breast:
29	chr9:22105883..22107388-chr9:22237172..22239101,2	MCF-7	breast:
30	chr9:22219852..22221736-chr9:22237176..22239431,2	MCF-7	breast:
31	chr9:22233059..22235536-chr9:22238140..22240172,2	MCF-7	breast:
32	chr9:22123972..22126695-chr9:22237756..22240192,3	MCF-7	breast:
33	chr9:22117727..22120443-chr9:22236352..22239028,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000099810	Chromatin interaction
ENSG00000147883	Chromatin interaction
ENSG00000240498	Chromatin interaction
ENSG00000147889	Chromatin interaction
ENSG00000229298	Chromatin interaction
ENSG00000264545	Chromatin interaction
ENSG00000266446	Chromatin interaction
ENSG00000236921	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11788928	0.82[EUR][1000 genomes]
rs11792897	0.82[EUR][1000 genomes]
rs11792932	0.82[EUR][1000 genomes]
rs12003808	0.87[EUR][1000 genomes]
rs16905769	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025797	0.87[EUR][1000 genomes]
rs2383209	0.87[EUR][1000 genomes]
rs2383212	0.91[EUR][1000 genomes]
rs2383213	0.87[EUR][1000 genomes]
rs4461984	0.87[EUR][1000 genomes]
rs4644346	0.82[EUR][1000 genomes]
rs62555450	0.87[EUR][1000 genomes]
rs62555451	0.87[EUR][1000 genomes]
rs62555452	0.82[EUR][1000 genomes]
rs62555455	0.87[EUR][1000 genomes]
rs62559460	0.82[EUR][1000 genomes]
rs62559467	0.82[EUR][1000 genomes]
rs62559468	0.87[EUR][1000 genomes]
rs62559469	0.82[EUR][1000 genomes]
rs62559470	0.82[EUR][1000 genomes]
rs62559471	0.82[EUR][1000 genomes]
rs62559472	0.91[EUR][1000 genomes]
rs62559473	0.91[EUR][1000 genomes]
rs62559474	0.91[EUR][1000 genomes]
rs62559475	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62559494	0.87[EUR][1000 genomes]
rs62559495	0.87[EUR][1000 genomes]
rs73444955	0.82[EUR][1000 genomes]
rs7853527	0.87[EUR][1000 genomes]
rs7853566	0.87[EUR][1000 genomes]
rs7859353	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7859407	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7872728	0.82[EUR][1000 genomes]
rs943399	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv892749	chr9:22125913-22244280	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1021264	chr9:22159622-22293804	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1033789	chr9:22183150-22266091	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1016067	chr9:22210874-22432654	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1015364	chr9:22211364-22416886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv540086	chr9:22211364-22416886	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22237000-22238600	Enhancers	Hela-S3	cervix
2	chr9:22237200-22239600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr9:22237200-22241800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:22237400-22239000	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr9:22237400-22239200	Enhancers	HUVEC	blood vessel
6	chr9:22237400-22239400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:22237400-22240200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:22237600-22238600	Flanking Active TSS	A549	lung
9	chr9:22237600-22238800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:22237600-22238800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr9:22237600-22239000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:22237600-22239000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr9:22237600-22239000	Enhancers	HSMM	muscle
14	chr9:22237600-22239000	Flanking Active TSS	NH-A	brain
15	chr9:22237600-22239000	Enhancers	NHDF-Ad	bronchial
16	chr9:22237600-22239000	Enhancers	NHLF	lung
17	chr9:22237600-22239400	Enhancers	Osteobl	bone
18	chr9:22237600-22240200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr9:22237600-22241400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:22237800-22239000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr9:22237800-22239600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:22238000-22238800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:22238000-22239000	Enhancers	Stomach Mucosa	stomach
24	chr9:22238000-22239600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr9:22238200-22238600	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr9:22238200-22238600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:22238200-22239000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:22238200-22239000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr9:22238200-22239000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:22238200-22241000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:22238400-22238800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr9:22238400-22238800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:22238400-22239000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:22238400-22239000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:22238400-22239200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr9:22238400-22239200	Flanking Active TSS	HSMMtube	muscle
37	chr9:22238400-22239400	Enhancers	Fetal Intestine Small	intestine
38	chr9:22238400-22239400	Flanking Active TSS	HMEC	breast
39	chr9:22238400-22239400	Flanking Active TSS	NHEK	skin

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