Variant report

Variant	rs9896411
Chromosome Location	chr17:19987610-19987611
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10083856	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1034904	0.82[AMR][1000 genomes]
rs11867585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868084	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11868116	0.82[EUR][1000 genomes]
rs11869616	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11870111	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11871651	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936443	0.82[EUR][1000 genomes]
rs16960697	0.82[EUR][1000 genomes]
rs1859407	0.81[EUR][1000 genomes]
rs2013443	0.82[EUR][1000 genomes]
rs2042046	0.82[EUR][1000 genomes]
rs2108980	0.82[AMR][1000 genomes]
rs2189709	0.81[EUR][1000 genomes]
rs2526463	0.81[EUR][1000 genomes]
rs2703795	0.80[EUR][1000 genomes]
rs28603224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28637614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28666381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28807825	0.84[AMR][1000 genomes]
rs34290687	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34291370	0.80[AMR][1000 genomes]
rs34401389	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35003563	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35313716	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36077949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862152	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3888318	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3909258	0.84[AMR][1000 genomes]
rs4005937	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4267380	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4479309	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4570919	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924801	0.82[AMR][1000 genomes]
rs4924803	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924806	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925065	0.82[AMR][1000 genomes]
rs4925066	0.82[AMR][1000 genomes]
rs4925067	0.82[AMR][1000 genomes]
rs4925069	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4925072	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4925073	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4925077	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925081	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925085	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925086	0.82[EUR][1000 genomes]
rs4925087	0.82[EUR][1000 genomes]
rs4925090	0.80[EUR][1000 genomes]
rs4925091	0.80[EUR][1000 genomes]
rs55705283	0.82[EUR][1000 genomes]
rs62066865	0.82[EUR][1000 genomes]
rs62066870	0.80[EUR][1000 genomes]
rs62067555	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587219	0.82[EUR][1000 genomes]
rs7207625	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7208025	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208365	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208635	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7209734	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7212500	0.82[EUR][1000 genomes]
rs7216599	0.82[EUR][1000 genomes]
rs7216794	0.82[EUR][1000 genomes]
rs7219908	0.82[EUR][1000 genomes]
rs7222984	0.83[EUR][1000 genomes]
rs7222987	0.80[EUR][1000 genomes]
rs7223305	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065337	0.81[AMR][1000 genomes]
rs8066143	0.82[EUR][1000 genomes]
rs8067545	0.80[AMR][1000 genomes]
rs8078716	0.82[EUR][1000 genomes]
rs8080649	0.80[EUR][1000 genomes]
rs888423	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs918227	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs918228	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889743	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9891739	0.84[AMR][1000 genomes]
rs9893832	0.82[EUR][1000 genomes]
rs9897246	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9897653	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898080	0.82[EUR][1000 genomes]
rs9901336	0.80[EUR][1000 genomes]
rs9901796	0.80[EUR][1000 genomes]
rs9902032	0.83[EUR][1000 genomes]
rs9907788	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9912775	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915758	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9944451	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
8	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
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	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
13	esv2762522	chr17:19976462-19996429	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9896411	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19976200-19988000	Weak transcription	Gastric	stomach
2	chr17:19976200-19989400	Weak transcription	Lung	lung
3	chr17:19977600-19989600	Weak transcription	K562	blood
4	chr17:19978000-19988200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:19979000-19988200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr17:19980200-19988200	Weak transcription	Brain Hippocampus Middle	brain
8	chr17:19980600-19994600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr17:19980800-19988200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr17:19980800-19990000	Weak transcription	A549	lung
11	chr17:19981000-19988000	Weak transcription	Aorta	Aorta
12	chr17:19981200-19993000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:19981600-19988200	Weak transcription	Adipose Nuclei	Adipose
14	chr17:19981800-19988600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr17:19982600-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:19983200-19988000	Weak transcription	Ovary	ovary
17	chr17:19983200-19993400	Weak transcription	Spleen	Spleen
18	chr17:19984000-19988200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr17:19984200-19988200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr17:19984200-19988200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr17:19984400-19987800	Weak transcription	GM12878-XiMat	blood
22	chr17:19984600-19988400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr17:19984800-19988000	Weak transcription	Brain Angular Gyrus	brain
24	chr17:19985000-19988000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:19985000-19989400	Weak transcription	Right Ventricle	heart
26	chr17:19985600-19988200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr17:19985600-19993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr17:19986200-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr17:19986400-19990600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr17:19986400-19991400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:19986800-19988400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr17:19986800-19988400	Weak transcription	Osteobl	bone
33	chr17:19986800-19989200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr17:19987000-19988000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr17:19987000-19988200	Weak transcription	HSMMtube	muscle
36	chr17:19987000-19994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr17:19987400-19987800	Weak transcription	NHDF-Ad	bronchial

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