Variant report

Variant	rs9897246
Chromosome Location	chr17:19965702-19965703
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19957236..19958763-chr17:19963646..19966262,2	K562	blood:

Extended variants
information (count: 116 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10083856	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1034904	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11867585	1.00[CEU][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11868084	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11868116	0.81[EUR][1000 genomes]
rs11869616	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11870111	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11871651	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs119672	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs12936443	0.81[EUR][1000 genomes]
rs12942179	0.89[CEU][hapmap]
rs1479129	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1638525	0.86[CHB][hapmap]
rs169412	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs16960697	0.81[EUR][1000 genomes]
rs175922	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1860302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2013443	0.81[EUR][1000 genomes]
rs203450	0.94[CHB][hapmap]
rs203457	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203458	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203460	0.94[CHB][hapmap]
rs203462	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203465	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203466	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203477	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203479	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203481	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs2042046	0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs2108978	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs2108979	0.83[AMR][1000 genomes]
rs2108980	0.86[AMR][1000 genomes]
rs28603224	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28637614	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28666381	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28807825	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34290687	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34291370	0.84[AMR][1000 genomes]
rs34401389	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35003563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35313716	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36077949	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3862152	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3888318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3909258	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs397969	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs4005937	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4267380	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4479309	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4570919	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4924801	0.86[AMR][1000 genomes]
rs4924803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924806	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4925060	0.87[CHB][hapmap]
rs4925065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs4925066	0.86[AMR][1000 genomes]
rs4925067	0.86[AMR][1000 genomes]
rs4925069	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4925072	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925073	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925079	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4925081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4925085	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4925086	0.81[EUR][1000 genomes]
rs4925087	0.81[EUR][1000 genomes]
rs55705283	0.81[EUR][1000 genomes]
rs62066865	0.81[EUR][1000 genomes]
rs62067555	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6587219	0.81[EUR][1000 genomes]
rs7207625	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7208025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7208365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7208635	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7209734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7211535	0.83[AMR][1000 genomes]
rs7212500	0.81[EUR][1000 genomes]
rs7216599	0.81[EUR][1000 genomes]
rs7216794	0.81[EUR][1000 genomes]
rs7219908	0.81[EUR][1000 genomes]
rs7222403	0.94[CHB][hapmap]
rs7222984	0.82[EUR][1000 genomes]
rs7223305	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8065337	0.85[AMR][1000 genomes]
rs8066143	0.81[EUR][1000 genomes]
rs8067545	0.84[AMR][1000 genomes]
rs8078716	0.81[EUR][1000 genomes]
rs850623	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs860335	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs888423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs918227	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs918228	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9889743	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9891739	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9893832	0.81[EUR][1000 genomes]
rs9896411	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9897653	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9898080	0.81[EUR][1000 genomes]
rs9902032	0.82[EUR][1000 genomes]
rs9907788	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9912775	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9915758	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944451	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[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	nsv1066594	chr17:19947874-19986671	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv543259	chr17:19947874-19986671	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9897246	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs9897246	AKAP10	cis	Lymphoblastoid	GTEx
rs9897246	AKAP10	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19943800-19965800	Weak transcription	Aorta	Aorta
2	chr17:19948200-19966400	Weak transcription	Brain Angular Gyrus	brain
3	chr17:19950800-19966400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:19957000-19965800	Weak transcription	Ovary	ovary
5	chr17:19957000-19967000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr17:19963000-19966000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr17:19963200-19966400	Weak transcription	Brain Hippocampus Middle	brain
8	chr17:19963600-19966200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr17:19963600-19966200	Weak transcription	Osteobl	bone
10	chr17:19963600-19966400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:19963600-19966400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr17:19963600-19966400	Weak transcription	Brain Anterior Caudate	brain
13	chr17:19963600-19966400	Weak transcription	HMEC	breast
14	chr17:19963600-19967000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr17:19963800-19967000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:19963800-19967200	Weak transcription	K562	blood
17	chr17:19964000-19966000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr17:19964200-19966600	Weak transcription	GM12878-XiMat	blood
19	chr17:19964200-19967000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr17:19964400-19966800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:19964800-19966600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:19965000-19966200	Weak transcription	NHDF-Ad	bronchial
23	chr17:19965000-19966400	Weak transcription	Hela-S3	cervix
24	chr17:19965200-19966200	Enhancers	A549	lung
25	chr17:19965200-19966400	Weak transcription	Adipose Nuclei	Adipose
26	chr17:19965600-19965800	Enhancers	Psoas Muscle	Psoas
27	chr17:19965600-19966400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:19965600-19967400	Enhancers	Primary monocytes fromperipheralblood	blood

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