Variant report

Variant	rs972966
Chromosome Location	chr17:20030992-20030993
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 150 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs11204422	0.88[ASN][1000 genomes]
rs11654025	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11869931	0.88[ASN][1000 genomes]
rs11870147	0.84[EUR][1000 genomes]
rs11870381	0.83[ASN][1000 genomes]
rs11870673	0.80[ASN][1000 genomes]
rs11871827	0.84[EUR][1000 genomes]
rs11871945	0.84[EUR][1000 genomes]
rs12451216	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12451841	0.90[ASN][1000 genomes]
rs12453332	0.85[ASN][1000 genomes]
rs12937827	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12942179	0.88[ASN][1000 genomes]
rs12947713	0.88[ASN][1000 genomes]
rs12949710	0.88[ASN][1000 genomes]
rs12952398	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1373147	0.84[EUR][1000 genomes]
rs1468953	0.88[ASN][1000 genomes]
rs1544421	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1561974	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17685923	0.88[ASN][1000 genomes]
rs17686798	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17686839	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17759923	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17759959	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1812934	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1985810	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1992562	0.84[EUR][1000 genomes]
rs2005722	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2013441	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2013576	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2034109	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2034110	0.80[ASN][1000 genomes]
rs2080673	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2107566	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2120282	0.84[EUR][1000 genomes]
rs2158473	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2165897	0.84[EUR][1000 genomes]
rs2189710	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2243732	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2263175	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2386429	0.84[EUR][1000 genomes]
rs2386485	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526458	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526460	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526462	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2526464	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2526467	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2526472	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526474	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526475	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526480	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2526483	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2526484	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2526488	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526490	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2703772	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703774	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703778	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703780	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703782	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703785	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703787	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2703789	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703790	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703791	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2703792	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2703794	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703799	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2703801	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2703802	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2703804	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2703806	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2703808	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703810	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2703815	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703816	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703817	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703818	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703820	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703821	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34089239	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34370440	0.90[ASN][1000 genomes]
rs34644796	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34712254	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34756775	0.88[ASN][1000 genomes]
rs35041742	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35124809	0.88[ASN][1000 genomes]
rs35156798	0.85[ASN][1000 genomes]
rs35191778	0.88[ASN][1000 genomes]
rs35244101	0.88[ASN][1000 genomes]
rs35493088	0.88[ASN][1000 genomes]
rs35770292	0.85[ASN][1000 genomes]
rs36051592	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3850783	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3850784	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3850785	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3940274	0.80[ASN][1000 genomes]
rs4341795	0.88[ASN][1000 genomes]
rs4346259	0.88[ASN][1000 genomes]
rs4350625	0.88[ASN][1000 genomes]
rs4471741	0.88[ASN][1000 genomes]
rs4588033	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924808	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924809	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924810	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4925075	0.88[ASN][1000 genomes]
rs4925076	0.88[ASN][1000 genomes]
rs4925078	0.88[ASN][1000 genomes]
rs4925082	0.87[ASN][1000 genomes]
rs4925088	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925089	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57146223	0.92[ASN][1000 genomes]
rs62067488	0.88[ASN][1000 genomes]
rs6587063	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7207611	0.84[EUR][1000 genomes]
rs7215803	0.88[ASN][1000 genomes]
rs7225249	0.88[ASN][1000 genomes]
rs7503407	0.88[ASN][1000 genomes]
rs8066705	0.83[ASN][1000 genomes]
rs8068484	0.87[ASN][1000 genomes]
rs8071665	0.84[EUR][1000 genomes]
rs8074047	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8074791	0.83[ASN][1000 genomes]
rs8075343	0.88[ASN][1000 genomes]
rs8079701	0.84[EUR][1000 genomes]
rs8081817	0.88[ASN][1000 genomes]
rs888424	0.88[ASN][1000 genomes]
rs9325894	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9892630	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9896221	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9896709	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9897328	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9900166	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9901125	0.90[ASN][1000 genomes]
rs9904928	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9905493	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9915059	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9915628	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	nsv833396	chr17:20029183-20150808	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs972966	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 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	chr17:20025400-20040400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:20025600-20031000	Weak transcription	Left Ventricle	heart
5	chr17:20025600-20034600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr17:20025800-20031000	Weak transcription	Hela-S3	cervix
7	chr17:20025800-20037600	Weak transcription	Ovary	ovary
8	chr17:20025800-20044400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:20026000-20031000	Weak transcription	Fetal Brain Female	brain
10	chr17:20026000-20031400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr17:20026200-20040000	Weak transcription	Aorta	Aorta
12	chr17:20026200-20049800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr17:20026600-20031200	Weak transcription	Fetal Brain Male	brain
14	chr17:20026600-20033200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr17:20027000-20031000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:20028800-20031600	Enhancers	Brain Angular Gyrus	brain
17	chr17:20029400-20033200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:20029400-20033600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:20029400-20042400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:20029600-20031000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr17:20029600-20031200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr17:20029600-20058800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr17:20029800-20031800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr17:20029800-20032000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr17:20029800-20040600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr17:20030000-20031000	Weak transcription	Brain Substantia Nigra	brain
27	chr17:20030000-20031200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr17:20030200-20031000	Weak transcription	Brain Hippocampus Middle	brain
29	chr17:20030200-20031200	Weak transcription	Brain Anterior Caudate	brain
30	chr17:20030200-20033000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr17:20030200-20043800	Weak transcription	Adipose Nuclei	Adipose
32	chr17:20030800-20031200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr17:20030800-20031800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr17:20030800-20031800	Enhancers	Fetal Heart	heart
35	chr17:20030800-20031800	Enhancers	Fetal Lung	lung
36	chr17:20030800-20032000	Enhancers	NHLF	lung
37	chr17:20030800-20032400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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