Variant report

Variant	rs7216599
Chromosome Location	chr17:20015600-20015601
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC144C-3	chr17:20015137-20016303	NONHSAT146542

Extended variants
information (count: 130 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10083856	0.81[EUR][1000 genomes]
rs10491107	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11204300	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11204423	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11653630	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11653869	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11654942	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11657161	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11867585	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs11868116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11869258	0.83[EUR][1000 genomes]
rs11871651	0.82[EUR][1000 genomes]
rs12603372	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12936443	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12938355	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12942568	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12942627	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12949481	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12950564	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1373146	0.83[EUR][1000 genomes]
rs16960697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1859407	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1974745	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992561	0.83[EUR][1000 genomes]
rs2013443	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2042046	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2107565	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2158472	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2189709	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2526459	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526463	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526465	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2526466	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2526476	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526477	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526478	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526481	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2526482	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2526486	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2703770	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2703771	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2703776	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2703777	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2703781	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703786	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703788	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2703795	0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2703800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2703803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2703805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2703807	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2703812	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2703814	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2703819	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28603224	0.82[EUR][1000 genomes]
rs28637614	0.82[EUR][1000 genomes]
rs28666381	0.82[EUR][1000 genomes]
rs34290687	0.82[EUR][1000 genomes]
rs34401389	0.82[EUR][1000 genomes]
rs35003563	0.82[EUR][1000 genomes]
rs36077949	0.82[EUR][1000 genomes]
rs3850779	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3850780	0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3862152	0.81[EUR][1000 genomes]
rs4005937	0.81[EUR][1000 genomes]
rs4267380	0.81[EUR][1000 genomes]
rs4570919	0.82[EUR][1000 genomes]
rs4924803	0.82[EUR][1000 genomes]
rs4924806	0.81[EUR][1000 genomes]
rs4925077	0.80[EUR][1000 genomes]
rs4925079	0.82[EUR][1000 genomes]
rs4925081	0.81[EUR][1000 genomes]
rs4925085	0.82[EUR][1000 genomes]
rs4925086	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925087	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925090	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4925091	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55705283	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57837691	0.84[EUR][1000 genomes]
rs62066865	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62066870	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62067555	0.82[EUR][1000 genomes]
rs6587219	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7207625	0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs7208025	0.82[EUR][1000 genomes]
rs7208365	0.82[EUR][1000 genomes]
rs7208635	0.82[EUR][1000 genomes]
rs7212500	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7216794	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7219615	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7219908	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7222984	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7222987	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7223305	0.82[EUR][1000 genomes]
rs7223476	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs733794	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs757494	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs757495	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8066143	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8071274	0.83[EUR][1000 genomes]
rs8078716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8080649	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs888423	0.81[EUR][1000 genomes]
rs918227	0.81[CHB][hapmap]
rs918228	0.82[EUR][1000 genomes]
rs9889743	0.81[EUR][1000 genomes]
rs9893832	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9896411	0.82[EUR][1000 genomes]
rs9897246	0.81[EUR][1000 genomes]
rs9897653	0.82[EUR][1000 genomes]
rs9898080	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9901336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9901796	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9902032	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9907516	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9907788	0.82[EUR][1000 genomes]
rs9912775	0.80[EUR][1000 genomes]
rs9915758	0.81[EUR][1000 genomes]
rs9944451	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv960437	chr17:20015227-20018343	Weak transcription Enhancers Strong transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7216599	AKAP10	cis	multi-tissue	Pritchard
rs7216599	AKAP10	cis	Lymphoblastoid	GTEx
rs7216599	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19999000-20032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr17:20002200-20018800	Weak transcription	Spleen	Spleen
3	chr17:20002200-20033400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr17:20007400-20024200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:20007600-20019800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr17:20007600-20020200	Weak transcription	Brain Angular Gyrus	brain
7	chr17:20007600-20024000	Weak transcription	Brain Substantia Nigra	brain
8	chr17:20007800-20017800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:20007800-20020200	Weak transcription	Brain Anterior Caudate	brain
10	chr17:20007800-20024000	Weak transcription	Brain Hippocampus Middle	brain
11	chr17:20009200-20024200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr17:20010800-20017200	Weak transcription	Primary T cells from cord blood	blood
13	chr17:20011800-20019200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr17:20012000-20018400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr17:20012600-20019800	Weak transcription	A549	lung
16	chr17:20013400-20016000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:20013600-20016400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:20014400-20019800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr17:20014400-20020000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr17:20014400-20024200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr17:20014400-20024400	Weak transcription	Ovary	ovary
22	chr17:20014400-20024800	Weak transcription	Aorta	Aorta
23	chr17:20014400-20025200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:20014600-20028800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr17:20015000-20016400	Strong transcription	Adipose Nuclei	Adipose
26	chr17:20015200-20016200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:20015200-20017800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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