Variant report

Variant	rs607562
Chromosome Location	chr11:100624538-100624539
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:100512013..100514802-chr11:100624099..100626304,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242165	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10128687	0.92[ASN][1000 genomes]
rs10431108	0.84[ASN][1000 genomes]
rs10895009	0.86[ASN][1000 genomes]
rs10895011	0.93[ASN][1000 genomes]
rs11224403	0.86[ASN][1000 genomes]
rs11224417	0.92[ASN][1000 genomes]
rs11224435	0.88[ASN][1000 genomes]
rs12286062	0.93[ASN][1000 genomes]
rs12291493	0.92[ASN][1000 genomes]
rs12419937	0.80[ASN][1000 genomes]
rs1502284	0.87[ASN][1000 genomes]
rs1532710	1.00[ASW][hapmap]
rs1847149	0.83[ASN][1000 genomes]
rs1847150	0.83[ASN][1000 genomes]
rs2298609	0.85[ASN][1000 genomes]
rs3858410	0.81[ASN][1000 genomes]
rs4312035	1.00[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.81[LWK][hapmap];0.82[TSI][hapmap]
rs4495864	0.97[ASN][1000 genomes]
rs4753984	0.92[ASN][1000 genomes]
rs4754695	0.83[ASN][1000 genomes]
rs4754697	0.93[ASN][1000 genomes]
rs4754698	0.99[ASN][1000 genomes]
rs486023	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs492237	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs604723	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs633185	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6590810	0.84[ASN][1000 genomes]
rs6590811	0.83[ASN][1000 genomes]
rs6590812	0.82[ASN][1000 genomes]
rs6590813	0.86[ASN][1000 genomes]
rs6590814	0.89[ASN][1000 genomes]
rs6590816	0.83[ASN][1000 genomes]
rs6590817	0.93[ASN][1000 genomes]
rs6590820	0.82[ASN][1000 genomes]
rs667575	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67143028	0.85[ASN][1000 genomes]
rs7103397	0.92[ASN][1000 genomes]
rs7105451	0.92[ASN][1000 genomes]
rs7106603	0.87[ASN][1000 genomes]
rs7112041	0.92[ASN][1000 genomes]
rs7114867	0.92[ASN][1000 genomes]
rs7125452	0.99[ASN][1000 genomes]
rs7130275	0.92[ASN][1000 genomes]
rs7926526	0.86[ASN][1000 genomes]
rs7928576	0.93[ASN][1000 genomes]
rs7930157	0.93[ASN][1000 genomes]
rs7952055	0.93[ASN][1000 genomes]
rs9919648	0.99[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	nsv1053430	chr11:99888390-100629136	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1042067	chr11:99889697-100629136	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1037689	chr11:99895378-100624599	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1040942	chr11:99895378-100629136	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1045190	chr11:99913193-100627395	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv541153	chr11:99913193-100627395	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv529454	chr11:99913394-100627255	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv898327	chr11:100569021-100631075	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs607562	ARHGAP42	cis	Artery Tibial	GTEx
rs607562	MMP8	cis	cerebellum	SCAN
rs607562	ARHGAP42	cis	cerebellum	SCAN
rs607562	TMEM133	cis	cerebellum	SCAN
rs607562	TMEM133	cis	parietal	SCAN
rs607562	DYNC2H1	cis	parietal	SCAN
rs607562	TMEM133	cis	Artery Tibial	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100612400-100630800	Weak transcription	Right Atrium	heart
2	chr11:100613000-100631600	Weak transcription	Ovary	ovary
3	chr11:100613200-100628400	Weak transcription	Fetal Kidney	kidney
4	chr11:100620800-100626800	Weak transcription	Liver	Liver
5	chr11:100620800-100628400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:100621000-100642400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:100621400-100631600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:100622200-100625800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr11:100622800-100624600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:100622800-100624600	Enhancers	Placenta	Placenta
11	chr11:100622800-100624800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr11:100622800-100624800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr11:100622800-100624800	Enhancers	HMEC	breast
14	chr11:100622800-100624800	Enhancers	NHEK	skin
15	chr11:100622800-100625200	Enhancers	Fetal Heart	heart
16	chr11:100623000-100624600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:100623000-100624600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:100623000-100624600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr11:100623000-100624800	Enhancers	Stomach Mucosa	stomach
20	chr11:100623000-100625000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr11:100623000-100625200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:100623000-100625200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr11:100623000-100625200	Enhancers	A549	lung
24	chr11:100623000-100626000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr11:100623000-100626400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:100623200-100624600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:100623200-100624600	Enhancers	Left Ventricle	heart
28	chr11:100623200-100624600	Enhancers	Right Ventricle	heart
29	chr11:100623200-100624800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr11:100623200-100625000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:100623200-100625400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr11:100623200-100626000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr11:100623200-100626400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr11:100623400-100624600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:100623400-100624800	Enhancers	H9 Cell Line	embryonic stem cell
36	chr11:100623400-100624800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr11:100623400-100625000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:100623400-100625400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr11:100623400-100632000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:100623600-100624600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr11:100623600-100624600	Enhancers	Hela-S3	cervix
42	chr11:100623600-100624800	Enhancers	Fetal Muscle Leg	muscle
43	chr11:100623600-100625000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr11:100623600-100625400	Enhancers	Duodenum Mucosa	Duodenum
45	chr11:100623800-100624600	Enhancers	Adipose Nuclei	Adipose
46	chr11:100623800-100624800	Enhancers	Fetal Intestine Large	intestine
47	chr11:100623800-100625200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:100623800-100625200	Enhancers	Fetal Intestine Small	intestine
49	chr11:100624000-100624600	Enhancers	Brain Substantia Nigra	brain
50	chr11:100624000-100624800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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