Variant report

Variant	rs9912042
Chromosome Location	chr17:60171223-60171224
allele	A/G
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	chr17:60171034..60173944-chr17:60180314..60182987,2	MCF-7	breast:
4	chr17:60171082..60173019-chr17:60180018..60181972,2	MCF-7	breast:
5	chr17:60163163..60166092-chr17:60169784..60172522,2	MCF-7	breast:
6	chr17:60139650..60144096-chr17:60169485..60173347,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10512493	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079463	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11079464	0.84[JPT][hapmap]
rs11652951	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11655971	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11869921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4592719	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4594309	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968410	0.84[JPT][hapmap]
rs4968473	0.83[JPT][hapmap]
rs4968477	0.84[JPT][hapmap]
rs55739298	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55742128	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56128308	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56202230	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57516918	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs686994	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs7213408	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8076927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8081812	0.84[JPT][hapmap]
rs9889676	0.83[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9912042	MRPS23	cis	parietal	SCAN
rs9912042	ANKFN1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60168200-60171400	Enhancers	HepG2	liver
2	chr17:60169600-60172800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr17:60169800-60171400	Enhancers	Liver	Liver
4	chr17:60170200-60171400	Enhancers	HSMM	muscle
5	chr17:60170200-60171800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr17:60170200-60172000	Enhancers	Hela-S3	cervix
7	chr17:60170200-60172000	Enhancers	NH-A	brain
8	chr17:60170200-60172000	Enhancers	NHEK	skin
9	chr17:60170200-60173000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:60170200-60174000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:60170200-60174000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:60170200-60174000	Enhancers	HMEC	breast
13	chr17:60170400-60171600	Enhancers	NHLF	lung
14	chr17:60170400-60171800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:60170400-60171800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr17:60170400-60172000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr17:60170400-60172000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr17:60170400-60172000	Enhancers	Duodenum Mucosa	Duodenum
19	chr17:60170400-60172000	Enhancers	NHDF-Ad	bronchial
20	chr17:60170400-60173200	Enhancers	Osteobl	bone
21	chr17:60170600-60171400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:60170600-60171400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:60170600-60171800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:60170600-60171800	Enhancers	Stomach Mucosa	stomach
25	chr17:60170600-60171800	Flanking Active TSS	A549	lung
26	chr17:60170600-60171800	Enhancers	HUVEC	blood vessel
27	chr17:60170600-60172000	Flanking Active TSS	GM12878-XiMat	blood
28	chr17:60170800-60171600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:60170800-60171600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:60170800-60171600	Enhancers	Aorta	Aorta
31	chr17:60170800-60171800	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr17:60171000-60171600	Enhancers	Primary B cells from peripheral blood	blood
33	chr17:60171000-60171800	Enhancers	Fetal Intestine Small	intestine
34	chr17:60171000-60171800	Enhancers	Spleen	Spleen
35	chr17:60171000-60175800	Weak transcription	K562	blood
36	chr17:60171200-60171400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr17:60171200-60171600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr17:60171200-60171800	Enhancers	Small Intestine	intestine
39	chr17:60171200-60172000	Enhancers	Pancreas	Pancrea
40	chr17:60171200-60173400	Weak transcription	HSMMtube	muscle

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