Variant report

Variant	rs11868429
Chromosome Location	chr17:20163616-20163617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12051550	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs12051844	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12051865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16942325	0.91[CHB][hapmap]
rs16959946	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs16960700	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16960715	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16960717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16960730	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]
rs16960735	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16964352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[ASN][1000 genomes]
rs1971043	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1971044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28550747	0.90[ASN][1000 genomes]
rs3751979	1.00[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];0.96[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764436	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs5025290	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[ASN][1000 genomes]
rs57110692	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61141789	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61660810	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6587060	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6587061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587218	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587221	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7207458	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7211948	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7213349	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7213816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7215097	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7215432	0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7218859	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73299658	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73301548	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73309111	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73981849	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8076627	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8077051	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8077852	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9895295	0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs9896190	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9899514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9901102	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9902683	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs9905976	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9908418	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs9911605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9913018	1.00[CHB][hapmap]
rs9913394	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9914219	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9941362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9941376	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
9	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
10	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
11	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
12	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
13	nsv1062124	chr17:20139384-20206601	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv543261	chr17:20139384-20206601	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1065758	chr17:20141912-20464366	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv543262	chr17:20141912-20464366	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	nsv1057389	chr17:20158343-20256498	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11868429	CYTSB	cis	parietal	SCAN
rs11868429	AKAP10	cis	Whole Blood	GTEx
rs11868429	ALDH3A1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20111600-20166000	Weak transcription	Right Ventricle	heart
2	chr17:20130600-20170000	Weak transcription	K562	blood
3	chr17:20130600-20170200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr17:20131800-20164400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr17:20136400-20209800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:20138400-20165200	Weak transcription	Primary B cells from cord blood	blood
7	chr17:20148200-20165000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr17:20148200-20165600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:20150400-20170200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:20150800-20165600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr17:20151200-20164000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr17:20151600-20164400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr17:20151600-20170800	Weak transcription	GM12878-XiMat	blood
14	chr17:20151600-20190000	Weak transcription	Colonic Mucosa	Colon
15	chr17:20151800-20165800	Weak transcription	HMEC	breast
16	chr17:20151800-20167000	Weak transcription	NH-A	brain
17	chr17:20152800-20169800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr17:20152800-20176200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:20155600-20165200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr17:20155800-20165000	Weak transcription	HUVEC	blood vessel
21	chr17:20157600-20165800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr17:20158000-20166200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr17:20158200-20165400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr17:20158800-20165600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr17:20159800-20165800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr17:20159800-20168200	Weak transcription	Fetal Heart	heart
27	chr17:20160200-20164200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr17:20160200-20165200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr17:20160400-20164600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:20160600-20164400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr17:20160600-20165000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr17:20160600-20165000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr17:20160600-20165800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:20160600-20166000	Strong transcription	Hela-S3	cervix
35	chr17:20161000-20164200	Strong transcription	Adipose Nuclei	Adipose
36	chr17:20161600-20164200	Strong transcription	Osteobl	bone
37	chr17:20161800-20165400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr17:20161800-20165600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr17:20161800-20180200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr17:20162000-20163800	Weak transcription	Fetal Muscle Leg	muscle
41	chr17:20162000-20164600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:20162000-20164600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:20162000-20164600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr17:20162000-20165000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr17:20162000-20165200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr17:20162000-20165600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr17:20162000-20165800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr17:20162000-20166000	Weak transcription	Small Intestine	intestine
49	chr17:20162000-20166200	Weak transcription	Aorta	Aorta
50	chr17:20162000-20172600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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