Variant report

Variant	rs8066449
Chromosome Location	chr17:67210267-67210268
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1011789	0.87[GIH][hapmap]
rs1024598	0.87[GIH][hapmap]
rs10775358	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10775359	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11077403	0.87[GIH][hapmap]
rs1158495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11652530	0.86[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs11656539	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12453914	0.91[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs12939282	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs12940298	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs12952117	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12953127	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1558166	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1968100	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1974576	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1974577	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2041171	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs2108738	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2190900	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2215148	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2364986	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2364991	0.83[GIH][hapmap]
rs2364992	0.87[GIH][hapmap]
rs2364993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3744489	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs4577157	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4603621	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs4968785	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4968838	0.86[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs4968839	0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[TSI][hapmap]
rs4968843	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4968849	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968851	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7208586	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs7210259	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7213831	0.86[CHB][hapmap];0.88[CHD][hapmap];0.83[TSI][hapmap]
rs7216899	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7217887	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs740518	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs740520	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8064583	0.87[GIH][hapmap]
rs8064595	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs8071373	0.87[GIH][hapmap]
rs8071611	0.82[GIH][hapmap]
rs8074654	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8077252	0.85[TSI][hapmap]
rs8077551	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8079981	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs8080693	0.87[GIH][hapmap]
rs8080863	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8081003	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs981452	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs981453	0.87[GIH][hapmap]
rs9891283	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9892172	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9894689	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898868	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9899837	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9902643	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9902996	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9904672	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9909083	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9909216	0.87[GIH][hapmap]
rs9911770	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9912127	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9916084	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9916693	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs997781	0.90[CHB][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv470598	chr17:67081830-67212595	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv575930	chr17:67120025-67212031	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv457888	chr17:67149973-67226643	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv575931	chr17:67149973-67226643	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
8	nsv575933	chr17:67153386-67215712	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv516799	chr17:67210267-67231581	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8066449	ABCA6	cis	parietal	SCAN
rs8066449	MRC2	cis	parietal	SCAN
rs8066449	ABCA8	cis	parietal	SCAN
rs8066449	ABCA6	cis	cerebellum	SCAN
rs8066449	CACNG5	cis	cerebellum	SCAN
rs8066449	TEX2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67144000-67236000	Weak transcription	Psoas Muscle	Psoas
2	chr17:67160600-67220000	Weak transcription	Fetal Lung	lung
3	chr17:67173400-67230000	Weak transcription	Pancreas	Pancrea
4	chr17:67189800-67221400	Weak transcription	Right Ventricle	heart
5	chr17:67192600-67219200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr17:67198200-67214800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr17:67201600-67215200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:67203400-67215000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:67205600-67215000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr17:67206000-67214800	Weak transcription	Adipose Nuclei	Adipose
11	chr17:67206000-67215200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr17:67207600-67247800	Weak transcription	Left Ventricle	heart
13	chr17:67207800-67215400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr17:67209000-67210400	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr17:67209200-67210400	ZNF genes & repeats	GM12878-XiMat	blood
16	chr17:67209400-67210600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr17:67209600-67216800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr17:67209800-67211400	Weak transcription	Liver	Liver
19	chr17:67209800-67214200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:67209800-67214800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr17:67209800-67215000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:67209800-67215000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:67209800-67215000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr17:67209800-67215200	Weak transcription	Lung	lung
25	chr17:67209800-67217800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr17:67209800-67223200	Weak transcription	Fetal Muscle Leg	muscle
27	chr17:67210000-67215000	Weak transcription	Ovary	ovary
28	chr17:67210000-67215400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:67210000-67218200	Weak transcription	Fetal Intestine Small	intestine
30	chr17:67210000-67219800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr17:67210200-67215000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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