Variant report

Variant	rs9934159
Chromosome Location	chr16:75617173-75617174
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	chr16:75611305..75613480-chr16:75615216..75617290,3	K562	blood:
2	chr16:75614933..75617785-chr16:75656182..75657692,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADAT1-1	chr16:75616487-75622358	XLOC_012011

Variant related genes	Relation type
ENSG00000065457	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11149842	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11149843	0.89[GIH][hapmap]
rs11643215	0.90[CEU][hapmap]
rs12446652	0.82[AMR][1000 genomes]
rs12595883	0.82[JPT][hapmap];0.87[MEX][hapmap]
rs12596033	0.87[JPT][hapmap]
rs12596724	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12596857	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12598094	0.82[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes]
rs12598741	0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12598751	0.83[MEX][hapmap]
rs12599322	0.82[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes]
rs12600066	0.82[AMR][1000 genomes]
rs12600271	0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs16940253	0.94[CHD][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16940467	0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16941533	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17764821	0.87[JPT][hapmap]
rs1865493	0.90[CEU][hapmap];0.93[JPT][hapmap]
rs1979717	0.87[JPT][hapmap];0.92[MEX][hapmap]
rs2082751	0.82[ASN][1000 genomes]
rs2164245	0.87[JPT][hapmap]
rs2242406	0.92[MEX][hapmap]
rs2289063	0.87[JPT][hapmap];0.92[MEX][hapmap]
rs2454867	0.82[EUR][1000 genomes]
rs2550904	0.80[JPT][hapmap]
rs2738794	0.83[EUR][1000 genomes]
rs2903106	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3736377	0.88[MEX][hapmap]
rs3743599	0.87[JPT][hapmap];0.96[MEX][hapmap]
rs3743603	0.82[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs3743605	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3784929	1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs3851741	0.92[MEX][hapmap]
rs41505349	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4887833	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4888436	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4888437	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4888440	0.87[JPT][hapmap]
rs5010692	1.00[CEU][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57252551	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57396453	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58273293	0.81[AMR][1000 genomes]
rs58597869	0.80[AMR][1000 genomes]
rs58719566	0.82[AMR][1000 genomes]
rs59907199	0.84[AMR][1000 genomes]
rs60393074	0.82[AMR][1000 genomes]
rs6564268	0.82[AMR][1000 genomes]
rs7186966	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7193066	0.80[CHD][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap]
rs73615030	0.94[ASN][1000 genomes]
rs74027438	0.85[AMR][1000 genomes]
rs7499759	0.80[AMR][1000 genomes]
rs8051241	0.93[ASN][1000 genomes]
rs8053219	0.84[MEX][hapmap]
rs8056968	0.80[AMR][1000 genomes]
rs8060972	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8061505	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8192516	0.80[AMR][1000 genomes]
rs963820	0.94[CHD][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
5	nsv532561	chr16:75519574-75636977	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9934159	ST3GAL2	cis	cerebellum	SCAN
rs9934159	ADAT1	cis	cerebellum	SCAN
rs9934159	ZNRF1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75601200-75624400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:75604200-75622600	Weak transcription	Right Atrium	heart
3	chr16:75607000-75623200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:75607600-75630800	Weak transcription	Fetal Brain Male	brain
5	chr16:75609000-75627800	Weak transcription	NHEK	skin
6	chr16:75610400-75634000	Weak transcription	Hela-S3	cervix
7	chr16:75610600-75622800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:75610600-75622800	Weak transcription	Fetal Heart	heart
9	chr16:75610600-75633400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr16:75610600-75635200	Weak transcription	Fetal Kidney	kidney
11	chr16:75611000-75624800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr16:75611400-75622600	Weak transcription	Right Ventricle	heart
13	chr16:75611400-75634000	Weak transcription	Colonic Mucosa	Colon
14	chr16:75611800-75628800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr16:75612000-75620400	Weak transcription	Pancreas	Pancrea
16	chr16:75612000-75622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr16:75612000-75627400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr16:75612000-75627400	Weak transcription	Psoas Muscle	Psoas
19	chr16:75612000-75631000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr16:75612000-75635600	Weak transcription	Small Intestine	intestine
21	chr16:75612400-75620200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr16:75612400-75624600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr16:75612400-75631000	Weak transcription	Gastric	stomach
24	chr16:75612400-75631200	Weak transcription	Esophagus	oesophagus
25	chr16:75612600-75622200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr16:75613200-75622800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr16:75613200-75622800	Weak transcription	Brain Germinal Matrix	brain
28	chr16:75613200-75624200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr16:75613200-75624400	Weak transcription	K562	blood
30	chr16:75613200-75624600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr16:75613200-75624800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr16:75613200-75624800	Weak transcription	NHLF	lung
33	chr16:75613200-75627200	Weak transcription	HepG2	liver
34	chr16:75613200-75627800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr16:75613200-75633400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr16:75613400-75619200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr16:75613400-75620400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr16:75613400-75624400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr16:75613400-75624400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr16:75613400-75624400	Weak transcription	HSMM	muscle
41	chr16:75613400-75624600	Weak transcription	NH-A	brain
42	chr16:75613400-75624800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr16:75613400-75624800	Weak transcription	NHDF-Ad	bronchial
44	chr16:75613400-75630800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr16:75613400-75635200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr16:75613600-75619600	Enhancers	Primary B cells from peripheral blood	blood
47	chr16:75613600-75622600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr16:75613600-75627400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr16:75613600-75630800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr16:75613600-75631000	Weak transcription	Placenta Amnion	Placenta Amnion

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