Variant report

Variant	rs2041171
Chromosome Location	chr17:67133352-67133353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:67127632..67130714-chr17:67132413..67134421,3	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10775358	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10775359	0.83[ASN][1000 genomes]
rs1158495	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11652530	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11656539	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11659091	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs12162136	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12453914	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12601388	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939282	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12940298	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12952117	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12953127	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1558166	0.86[ASN][1000 genomes]
rs16973567	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1968100	0.85[ASN][1000 genomes]
rs1974576	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1974577	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1990335	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2041170	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108738	0.83[ASN][1000 genomes]
rs2190900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215148	0.86[ASN][1000 genomes]
rs2364986	0.86[ASN][1000 genomes]
rs2364993	0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs3744489	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4141177	0.82[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4334355	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4577157	0.84[ASN][1000 genomes]
rs4603621	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968785	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4968838	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968839	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968843	0.86[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4968849	0.87[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[ASN][1000 genomes]
rs4968851	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs5025273	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs6501183	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7207609	0.83[EUR][1000 genomes]
rs7208586	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7210259	0.90[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7213831	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7214079	0.81[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7216899	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7217887	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs740518	0.86[ASN][1000 genomes]
rs740520	0.87[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7503217	0.84[EUR][1000 genomes]
rs763920	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs8064595	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8066449	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs8074654	0.87[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs8077252	0.86[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8077551	0.87[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs8078314	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8079981	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8080863	0.87[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs8081003	0.80[ASN][1000 genomes]
rs9303012	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs976698	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs981452	0.87[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9892172	0.85[ASN][1000 genomes]
rs9898868	0.85[ASN][1000 genomes]
rs9899837	0.85[ASN][1000 genomes]
rs9902643	0.86[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9904672	0.85[ASN][1000 genomes]
rs9911770	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9912127	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs9916084	0.83[ASN][1000 genomes]
rs9916693	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs997781	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2041171	ABCA6	cis	cerebellum	SCAN
rs2041171	ABCA9	cis	parietal	SCAN
rs2041171	MRC2	cis	parietal	SCAN
rs2041171	CACNG5	cis	cerebellum	SCAN
rs2041171	ABCA6	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67077800-67137800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr17:67092200-67137600	Weak transcription	Brain Anterior Caudate	brain
3	chr17:67096200-67143400	Weak transcription	Psoas Muscle	Psoas
4	chr17:67096400-67134000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr17:67097000-67133800	Weak transcription	Colon Smooth Muscle	Colon
6	chr17:67101200-67143400	Weak transcription	Pancreas	Pancrea
7	chr17:67114600-67162800	Weak transcription	Brain Angular Gyrus	brain
8	chr17:67115600-67134000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:67120000-67138000	Weak transcription	Small Intestine	intestine
10	chr17:67121800-67137800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr17:67123800-67136400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:67124600-67137600	Weak transcription	Fetal Stomach	stomach
13	chr17:67124800-67150000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr17:67127000-67143400	Weak transcription	Fetal Intestine Large	intestine
15	chr17:67127000-67150600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr17:67127200-67138000	Weak transcription	Stomach Mucosa	stomach
17	chr17:67127600-67137800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr17:67128200-67134400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:67128200-67137200	Weak transcription	Brain Substantia Nigra	brain
20	chr17:67128400-67134000	Strong transcription	Adipose Nuclei	Adipose
21	chr17:67128800-67133600	Strong transcription	Liver	Liver
22	chr17:67129000-67134400	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr17:67129400-67133800	Weak transcription	Aorta	Aorta
24	chr17:67129800-67137000	Weak transcription	Fetal Brain Male	brain
25	chr17:67130200-67134400	Strong transcription	NHDF-Ad	bronchial
26	chr17:67130600-67133800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr17:67130600-67146200	Weak transcription	Lung	lung
28	chr17:67131600-67134600	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr17:67132000-67137800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr17:67132000-67151600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr17:67132200-67133600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr17:67132200-67133800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr17:67132200-67134000	Weak transcription	Left Ventricle	heart
34	chr17:67132200-67137600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr17:67132200-67137600	Weak transcription	Brain Hippocampus Middle	brain
36	chr17:67132200-67137600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr17:67132200-67137800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr17:67132400-67136800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:67133200-67134000	Strong transcription	Ovary	ovary
40	chr17:67133200-67134200	ZNF genes & repeats	Fetal Lung	lung
41	chr17:67133200-67134600	ZNF genes & repeats	Fetal Muscle Leg	muscle

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