Variant report

Variant	rs12949485
Chromosome Location	chr17:20021661-20021662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20020458..20023220-chr17:20026359..20029161,2	K562	blood:

Extended variants
information (count: 146 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1009082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10438824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654025	0.85[CEU][hapmap]
rs11870147	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11871827	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11871945	1.00[ASN][1000 genomes]
rs12449914	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12450857	1.00[CHB][hapmap]
rs12451216	0.82[AMR][1000 genomes]
rs12453720	1.00[CHB][hapmap]
rs12935996	1.00[YRI][hapmap]
rs12937827	1.00[ASN][1000 genomes]
rs12941200	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12943904	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12947950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12948178	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952398	1.00[ASN][1000 genomes]
rs1373147	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1544421	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1561974	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1638527	1.00[CHB][hapmap]
rs17604987	1.00[CHB][hapmap]
rs17686622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17686798	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs17686839	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17759609	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17759923	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17759959	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs1812934	0.85[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1985810	1.00[ASN][1000 genomes]
rs1992562	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2013441	0.84[CEU][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2013576	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2034109	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs203475	1.00[CHB][hapmap]
rs203480	1.00[CHB][hapmap]
rs2058971	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2080673	1.00[ASN][1000 genomes]
rs2107566	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2108981	1.00[CHB][hapmap]
rs2120282	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2158473	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2165897	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs2189710	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2243732	1.00[ASN][1000 genomes]
rs2263175	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2386429	1.00[ASN][1000 genomes]
rs2386485	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2526458	1.00[ASN][1000 genomes]
rs2526460	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2526462	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2526464	1.00[ASN][1000 genomes]
rs2526467	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2526468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526470	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526472	1.00[ASN][1000 genomes]
rs2526473	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526474	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2526475	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2526480	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2526483	1.00[ASN][1000 genomes]
rs2526484	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2526488	1.00[ASN][1000 genomes]
rs2526490	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs2526491	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526492	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703772	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2703773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703774	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703778	1.00[ASN][1000 genomes]
rs2703779	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703780	1.00[ASN][1000 genomes]
rs2703782	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703784	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703785	1.00[ASN][1000 genomes]
rs2703787	1.00[ASN][1000 genomes]
rs2703789	1.00[ASN][1000 genomes]
rs2703790	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703791	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703792	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703794	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703797	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703799	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2703801	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703802	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2703804	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703806	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703808	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703810	1.00[ASN][1000 genomes]
rs2703811	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2703813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703815	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703816	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703817	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703818	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2703820	1.00[ASN][1000 genomes]
rs2703821	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34089239	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34644796	1.00[ASN][1000 genomes]
rs34712254	1.00[ASN][1000 genomes]
rs35103332	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3850783	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3850784	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs3850785	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3862151	1.00[CHB][hapmap]
rs4588033	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4924802	1.00[CHB][hapmap]
rs4924808	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs4924809	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4924810	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs4925084	1.00[CHB][hapmap]
rs4925089	1.00[ASN][1000 genomes]
rs62066869	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62067558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587063	0.83[ASN][1000 genomes]
rs6587064	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7207611	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7207817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7223488	0.83[ASN][1000 genomes]
rs8068720	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs8070401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8071665	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs8074047	1.00[ASN][1000 genomes]
rs8079701	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8080827	1.00[CHB][hapmap]
rs9325894	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9892630	1.00[ASN][1000 genomes]
rs9896221	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9896709	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9897328	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9900166	1.00[ASN][1000 genomes]
rs9904928	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9905493	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9915059	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12949485	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19999000-20032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr17:20002200-20033400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr17:20007400-20024200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:20007600-20024000	Weak transcription	Brain Substantia Nigra	brain
5	chr17:20007800-20024000	Weak transcription	Brain Hippocampus Middle	brain
6	chr17:20009200-20024200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr17:20014400-20024200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:20014400-20024400	Weak transcription	Ovary	ovary
9	chr17:20014400-20024800	Weak transcription	Aorta	Aorta
10	chr17:20014400-20025200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr17:20014600-20028800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:20016000-20028800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:20016400-20024400	Weak transcription	Adipose Nuclei	Adipose
14	chr17:20016400-20028600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:20017400-20026200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr17:20018200-20025200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:20018400-20025000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr17:20020200-20023600	Weak transcription	Fetal Brain Male	brain
19	chr17:20020600-20023800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:20020600-20024200	Weak transcription	Brain Angular Gyrus	brain
21	chr17:20020600-20024200	Weak transcription	Brain Anterior Caudate	brain
22	chr17:20020600-20024200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr17:20020600-20024200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr17:20020600-20024800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:20020600-20025200	Weak transcription	A549	lung
26	chr17:20021600-20023200	Strong transcription	Monocytes-CD14+_RO01746	blood

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