Variant report

Variant	rs16960983
Chromosome Location	chr17:18104568-18104569
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18087388..18090875-chr17:18103511..18106213,4	K562	blood:

Variant related genes	Relation type
ENSG00000266677	Chromatin interaction
ENSG00000091542	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10048161	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451244	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652964	1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs11653988	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654146	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654177	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654741	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655731	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11655797	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656035	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11657194	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11658477	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs11868832	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868886	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11869582	0.80[CEU][hapmap]
rs11871039	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11871491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12449313	0.94[GIH][hapmap]
rs12600694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16960980	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960990	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960996	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961153	0.94[GIH][hapmap]
rs2015336	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071242	0.90[GIH][hapmap]
rs2290502	0.90[GIH][hapmap]
rs2290503	0.90[GIH][hapmap]
rs2294913	0.94[GIH][hapmap]
rs28364628	0.90[GIH][hapmap]
rs28811342	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34474249	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36058389	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3817992	0.94[GIH][hapmap]
rs3829956	0.94[GIH][hapmap]
rs55918833	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58441148	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59354912	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60285171	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072464	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62072465	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072466	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072467	0.92[EUR][1000 genomes]
rs62072468	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072496	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62072497	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62072498	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072500	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073602	0.89[EUR][1000 genomes]
rs62073603	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62073604	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62073605	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62073606	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62073607	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073608	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073609	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073611	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62073615	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62073649	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073650	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207276	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7215678	0.90[GIH][hapmap]
rs735960	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7498	0.90[GIH][hapmap]
rs8065026	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs8069094	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077577	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9909104	1.00[GIH][hapmap]
rs9913139	0.90[GIH][hapmap]
rs9916193	0.88[EUR][1000 genomes]
rs997315	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[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	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1062828	chr17:18098110-18136330	Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv543245	chr17:18098110-18136330	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs16960983	SHMT1	cis	cerebellum	SCAN
rs16960983	PLD6	cis	cerebellum	SCAN
rs16960983	TRPV2	cis	cerebellum	SCAN
rs16960983	LOC162632	cis	parietal	SCAN
rs16960983	FLII	cis	cerebellum	SCAN
rs16960983	LOC162632	cis	cerebellum	SCAN
rs16960983	SHMT1	cis	lymphoblastoid	seeQTL
rs16960983	EPN2	cis	parietal	SCAN
rs16960983	SLC47A1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18091200-18104600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:18091400-18114000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:18091800-18114400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr17:18094200-18114600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:18094400-18114600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr17:18094600-18114600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:18095000-18108600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr17:18095000-18114600	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr17:18095000-18114800	Strong transcription	Fetal Thymus	thymus
10	chr17:18095400-18116000	Strong transcription	Fetal Stomach	stomach
11	chr17:18095600-18114600	Strong transcription	Dnd41	blood
12	chr17:18095800-18108600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr17:18096200-18114400	Strong transcription	Primary T cells from cord blood	blood
14	chr17:18096200-18114600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:18096400-18104800	Strong transcription	Hela-S3	cervix
16	chr17:18096800-18114600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr17:18097000-18105000	Strong transcription	A549	lung
18	chr17:18097000-18108600	Strong transcription	Brain Germinal Matrix	brain
19	chr17:18097000-18114600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr17:18097200-18114600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr17:18097600-18114600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr17:18097800-18104800	Strong transcription	Primary hematopoietic stem cells	blood
23	chr17:18097800-18114600	Strong transcription	Fetal Brain Female	brain
24	chr17:18098000-18104600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr17:18098000-18105000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr17:18098000-18114600	Strong transcription	Primary B cells from cord blood	blood
27	chr17:18098000-18114600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr17:18098000-18114600	Strong transcription	Fetal Muscle Leg	muscle
29	chr17:18098200-18105800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:18098200-18107400	Strong transcription	Fetal Lung	lung
31	chr17:18100600-18104600	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr17:18100800-18104800	Genic enhancers	Brain Inferior Temporal Lobe	brain
33	chr17:18100800-18104800	Genic enhancers	Right Ventricle	heart
34	chr17:18101000-18104600	Genic enhancers	Brain Cingulate Gyrus	brain
35	chr17:18101000-18108600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:18101200-18108400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:18101200-18114400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr17:18101600-18114600	Strong transcription	Thymus	Thymus
39	chr17:18101600-18115400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:18101800-18105600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr17:18101800-18105800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr17:18101800-18108200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr17:18101800-18108400	Weak transcription	Fetal Brain Male	brain
44	chr17:18101800-18109400	Weak transcription	HSMMtube	muscle
45	chr17:18102000-18108200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr17:18102000-18108600	Weak transcription	K562	blood
47	chr17:18102000-18108800	Weak transcription	Colonic Mucosa	Colon
48	chr17:18102000-18114600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr17:18102000-18116200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr17:18102200-18104600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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