Variant report

Variant	rs16960730
Chromosome Location	chr17:20129491-20129492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20025221..20027004-chr17:20127712..20130710,2	MCF-7	breast:
2	chr17:20058383..20060895-chr17:20129200..20131943,2	K562	blood:
3	chr17:20024691..20025538-chr17:20129010..20129692,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11868429	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12051550	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs12051844	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12051865	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16942325	0.90[CHB][hapmap]
rs16959946	1.00[CHB][hapmap]
rs16960700	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16960715	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16960717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16960735	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16964352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs1971043	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1971044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3751979	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3764436	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs5025290	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs57110692	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61141789	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61660810	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587060	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587061	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587218	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587221	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7207458	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7211948	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7213349	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7213816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7215097	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7215432	0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7218859	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73299658	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73301548	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73309111	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73981849	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8076627	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8077051	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8077852	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9895295	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs9896190	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9899514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9901102	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9901484	0.88[ASN][1000 genomes]
rs9902683	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs9905976	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9908032	0.88[ASN][1000 genomes]
rs9908418	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs9909156	0.92[ASN][1000 genomes]
rs9911605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9913018	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9913394	0.89[EUR][1000 genomes]
rs9914219	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9941362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9941376	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv833396	chr17:20029183-20150808	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS 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
9	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1063833	chr17:20088333-20206601	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
14	nsv1065363	chr17:20118499-20162888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1059774	chr17:20118499-20163560	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16960730	ALDH3A1	cis	parietal	SCAN
rs16960730	AKAP10	cis	Whole Blood	GTEx
rs16960730	CYTSB	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20106800-20130200	Weak transcription	Fetal Stomach	stomach
2	chr17:20106800-20131400	Weak transcription	Fetal Intestine Large	intestine
3	chr17:20107600-20131600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr17:20108000-20130200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:20108000-20130200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr17:20108400-20131400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr17:20109600-20135200	Weak transcription	Gastric	stomach
8	chr17:20110800-20130400	Weak transcription	HSMMtube	muscle
9	chr17:20111600-20166000	Weak transcription	Right Ventricle	heart
10	chr17:20112000-20130200	Weak transcription	NH-A	brain
11	chr17:20115400-20135000	Weak transcription	Fetal Intestine Small	intestine
12	chr17:20115600-20131600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:20115600-20132800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr17:20115800-20131400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr17:20116000-20130200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:20117000-20130800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr17:20117200-20131600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:20118600-20134200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr17:20120800-20131600	Weak transcription	GM12878-XiMat	blood
20	chr17:20125200-20144000	Weak transcription	Small Intestine	intestine
21	chr17:20125400-20129600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr17:20125600-20130600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr17:20126400-20134000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr17:20127000-20130600	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr17:20127000-20130800	Enhancers	Brain Hippocampus Middle	brain
26	chr17:20127000-20130800	Enhancers	Brain Substantia Nigra	brain
27	chr17:20127000-20131000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr17:20127000-20132000	Genic enhancers	Hela-S3	cervix
29	chr17:20127200-20130600	Enhancers	A549	lung
30	chr17:20127200-20130800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr17:20127200-20130800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr17:20127200-20130800	Enhancers	Brain Angular Gyrus	brain
33	chr17:20127200-20132000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:20127200-20132800	Enhancers	Brain Cingulate Gyrus	brain
35	chr17:20127600-20130000	Weak transcription	K562	blood
36	chr17:20127800-20130400	Weak transcription	NHLF	lung
37	chr17:20128000-20130000	Weak transcription	Aorta	Aorta
38	chr17:20128000-20130400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr17:20128000-20130600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr17:20128200-20130400	Weak transcription	Colon Smooth Muscle	Colon
41	chr17:20128400-20130600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr17:20128800-20130000	Weak transcription	Osteobl	bone
43	chr17:20128800-20130200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:20128800-20130200	Weak transcription	Esophagus	oesophagus
45	chr17:20128800-20130400	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr17:20128800-20157000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr17:20129000-20130000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr17:20129000-20130000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr17:20129000-20130000	Weak transcription	Brain Germinal Matrix	brain
50	chr17:20129000-20130000	Weak transcription	Fetal Brain Male	brain

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