Variant report

Variant	rs1034904
Chromosome Location	chr17:19927699-19927700
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19927266..19929867-chr17:19933852..19935376,2	K562	blood:
2	chr17:19915750..19917622-chr17:19925482..19928326,2	K562	blood:
3	chr17:19920482..19924140-chr17:19925056..19928088,3	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10083856	0.84[AMR][1000 genomes]
rs11204421	0.81[ASN][1000 genomes]
rs11867585	0.91[JPT][hapmap];0.82[AMR][1000 genomes]
rs11871651	0.84[AMR][1000 genomes]
rs119672	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1479129	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs1638525	0.86[CHB][hapmap]
rs169412	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs16960644	0.89[ASN][1000 genomes]
rs16960697	0.80[MEX][hapmap]
rs175922	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs1860302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203450	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203457	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203458	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203460	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203462	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203465	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203466	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203477	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203479	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203481	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs2042046	0.85[JPT][hapmap]
rs2107565	0.80[MEX][hapmap]
rs2108978	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs2108979	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108980	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2703805	0.80[MEX][hapmap]
rs2703807	0.80[MEX][hapmap]
rs2703814	0.80[MEX][hapmap]
rs28603224	0.82[AMR][1000 genomes]
rs28637614	0.82[AMR][1000 genomes]
rs28666381	0.82[AMR][1000 genomes]
rs28807825	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34290687	0.81[AMR][1000 genomes]
rs34291370	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34401389	0.81[AMR][1000 genomes]
rs35003563	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes]
rs36034566	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36077949	0.82[AMR][1000 genomes]
rs3862152	0.86[AMR][1000 genomes]
rs3888318	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3909258	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs397969	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs4005937	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4267380	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4479308	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4479309	0.83[AMR][1000 genomes]
rs4570919	0.83[AMR][1000 genomes]
rs4924801	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924803	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes]
rs4924806	0.83[AMR][1000 genomes]
rs4925060	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs4925065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925066	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925067	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925069	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925072	0.84[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.86[AMR][1000 genomes]
rs4925073	0.85[AMR][1000 genomes]
rs4925077	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4925079	0.82[AMR][1000 genomes]
rs4925081	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes]
rs4925085	0.80[AMR][1000 genomes]
rs4925090	0.80[MEX][hapmap]
rs56142708	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62067555	0.83[AMR][1000 genomes]
rs7207625	0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes]
rs7208025	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes]
rs7208365	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes]
rs7208635	0.83[AMR][1000 genomes]
rs7209734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7211535	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7215514	0.82[ASN][1000 genomes]
rs7218708	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7222403	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7223305	0.83[AMR][1000 genomes]
rs8065337	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8067545	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs850623	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs860335	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs888423	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes]
rs918227	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs918228	0.83[AMR][1000 genomes]
rs9889743	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9891739	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9893832	0.80[MEX][hapmap]
rs9896411	0.82[AMR][1000 genomes]
rs9897246	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9897653	0.81[AMR][1000 genomes]
rs9906625	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9907788	0.85[AMR][1000 genomes]
rs9909009	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9912775	0.81[AMR][1000 genomes]
rs9915758	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9916675	0.82[ASN][1000 genomes]
rs9944451	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1034904	AKAP10	cis	multi-tissue	Pritchard
rs1034904	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs1034904	C2orf81	trans	cerebellum	SCAN
rs1034904	CYTSB	cis	cerebellum	SCAN
rs1034904	AKAP10	cis	Lymphoblastoid	GTEx
rs1034904	AKAP10	cis	lymphoblastoid	seeQTL
rs1034904	TMEM11	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19914600-19928000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr17:19914600-19938400	Weak transcription	Brain Hippocampus Middle	brain
3	chr17:19921600-19928000	Weak transcription	Brain Anterior Caudate	brain
4	chr17:19921600-19931600	Weak transcription	Ovary	ovary
5	chr17:19922200-19935800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:19922400-19928400	Weak transcription	Aorta	Aorta
7	chr17:19923400-19930800	Weak transcription	K562	blood
8	chr17:19923400-19956600	Weak transcription	A549	lung
9	chr17:19923600-19946400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr17:19926200-19932400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr17:19926400-19947000	Weak transcription	Brain Angular Gyrus	brain
12	chr17:19926800-19930200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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