Variant report

Variant	rs9893015
Chromosome Location	chr17:60171950-60171951
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60169141..60172371-chr17:60175299..60177766,3	MCF-7	breast:
2	chr17:60171136..60172772-chr17:60213380..60215934,2	K562	blood:
3	chr17:60161818..60164502-chr17:60171799..60173649,2	MCF-7	breast:
4	chr17:60171034..60173944-chr17:60180314..60182987,2	MCF-7	breast:
5	chr17:60171082..60173019-chr17:60180018..60181972,2	MCF-7	breast:
6	chr17:60163163..60166092-chr17:60169784..60172522,2	MCF-7	breast:
7	chr17:60139650..60144096-chr17:60169485..60173347,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10401014	0.85[ASW][hapmap]
rs11079460	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs11079462	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11658522	0.93[GIH][hapmap]
rs12150361	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12936713	0.82[CHB][hapmap];0.86[GIH][hapmap]
rs12943168	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952786	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221376	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7223780	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359581	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7407011	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9303456	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9891843	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062816	chr17:60074670-60470465	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	esv2753884	chr17:60077852-60190630	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv2755037	chr17:60086508-60386211	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3415630	chr17:60124819-60401635	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9893015	CA4	cis	cerebellum	SCAN
rs9893015	RNF43	cis	parietal	SCAN
rs9893015	MED13	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60169600-60172800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr17:60170200-60172000	Enhancers	Hela-S3	cervix
3	chr17:60170200-60172000	Enhancers	NH-A	brain
4	chr17:60170200-60172000	Enhancers	NHEK	skin
5	chr17:60170200-60173000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr17:60170200-60174000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:60170200-60174000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:60170200-60174000	Enhancers	HMEC	breast
9	chr17:60170400-60172000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr17:60170400-60172000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr17:60170400-60172000	Enhancers	Duodenum Mucosa	Duodenum
12	chr17:60170400-60172000	Enhancers	NHDF-Ad	bronchial
13	chr17:60170400-60173200	Enhancers	Osteobl	bone
14	chr17:60170600-60172000	Flanking Active TSS	GM12878-XiMat	blood
15	chr17:60171000-60175800	Weak transcription	K562	blood
16	chr17:60171200-60172000	Enhancers	Pancreas	Pancrea
17	chr17:60171200-60173400	Weak transcription	HSMMtube	muscle
18	chr17:60171400-60172000	Flanking Active TSS	HepG2	liver
19	chr17:60171400-60172600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr17:60171400-60173000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:60171400-60173400	Weak transcription	HSMM	muscle
22	chr17:60171600-60172600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr17:60171600-60173200	Weak transcription	Aorta	Aorta
24	chr17:60171600-60175000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr17:60171800-60172000	Enhancers	A549	lung
26	chr17:60171800-60173400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr17:60171800-60174000	Enhancers	Liver	Liver
28	chr17:60171800-60175200	Weak transcription	Fetal Intestine Small	intestine
29	chr17:60171800-60175600	Weak transcription	Small Intestine	intestine
30	chr17:60171800-60176200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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