Variant report

Variant	rs4985518
Chromosome Location	chr16:69787158-69787159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:69787153-69787314	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:69785030..69792317-chr16:69794435..69797821,11	MCF-7	breast:
2	chr16:69742300..69746801-chr16:69786779..69790470,7	MCF-7	breast:
3	chr16:69757296..69762552-chr16:69785671..69789636,11	K562	blood:
4	chr16:69756628..69762611-chr16:69781362..69792848,24	MCF-7	breast:
5	chr16:69747305..69749141-chr16:69786913..69788664,2	MCF-7	breast:
6	chr16:69758127..69765240-chr16:69786072..69790209,13	K562	blood:

No data

Variant related genes	Relation type
NOB1	TF binding region
ENSG00000198373	Chromatin interaction
ENSG00000262136	Chromatin interaction
ENSG00000238683	Chromatin interaction
ENSG00000261602	Chromatin interaction
ENSG00000181019	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10048108	0.84[EUR][1000 genomes]
rs10163235	0.84[EUR][1000 genomes]
rs10454066	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs10500551	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs10852458	1.00[CEU][hapmap]
rs11075728	1.00[CEU][hapmap]
rs11075733	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11075734	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1139178	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11639947	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs11641233	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap]
rs11641521	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11642030	1.00[CEU][hapmap]
rs11643926	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11644838	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11644914	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12232410	0.95[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs12446201	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12447883	0.82[EUR][1000 genomes]
rs12595869	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs12596679	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12596823	1.00[CEU][hapmap]
rs12925371	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1437135	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs16958970	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs16959025	1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs16959035	0.83[EUR][1000 genomes]
rs1800566	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs1865965	0.82[EUR][1000 genomes]
rs2196574	0.85[EUR][1000 genomes]
rs2361838	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs2361839	0.84[EUR][1000 genomes]
rs3169315	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap]
rs3743673	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3811349	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4078387	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4341733	0.81[ASW][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap]
rs4464069	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4497676	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4580150	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985418	0.82[MKK][hapmap]
rs4985523	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55701476	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55863174	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55992518	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56282083	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57488237	0.83[EUR][1000 genomes]
rs57518557	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57565297	0.82[EUR][1000 genomes]
rs59295369	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60231938	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61426398	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6499253	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499255	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6499257	0.81[ASW][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap]
rs689455	0.85[EUR][1000 genomes]
rs7186002	0.85[EUR][1000 genomes]
rs7189424	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7196943	1.00[CEU][hapmap]
rs7198242	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs73579458	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73579497	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74029403	0.82[EUR][1000 genomes]
rs8045682	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8046314	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs8054096	0.82[EUR][1000 genomes]
rs8059345	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9788837	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs9921045	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs9933526	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv524364	chr16:69745145-69803443	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4985518	FAM96B	cis	parietal	SCAN
rs4985518	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs4985518	SLC7A6	cis	cerebellum	SCAN
rs4985518	HPR	cis	cerebellum	SCAN
rs4985518	TPPP3	cis	parietal	SCAN
rs4985518	HPR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69761800-69787400	Weak transcription	Right Atrium	heart
2	chr16:69770400-69788000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:69773000-69787200	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr16:69776200-69787200	Weak transcription	Psoas Muscle	Psoas
5	chr16:69780600-69788000	Weak transcription	Stomach Mucosa	stomach
6	chr16:69781800-69787200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr16:69783000-69788000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr16:69783200-69787200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr16:69783200-69787800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr16:69783400-69787200	Weak transcription	Fetal Heart	heart
11	chr16:69783400-69787200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr16:69783400-69787400	Weak transcription	Colonic Mucosa	Colon
13	chr16:69783400-69787400	Weak transcription	Right Ventricle	heart
14	chr16:69783600-69787200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr16:69783600-69788000	Weak transcription	Small Intestine	intestine
16	chr16:69783600-69788200	Weak transcription	Aorta	Aorta
17	chr16:69783800-69787800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr16:69784200-69787200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr16:69784600-69787400	Weak transcription	Brain Substantia Nigra	brain
20	chr16:69784600-69787800	Weak transcription	Esophagus	oesophagus
21	chr16:69784600-69788000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr16:69784800-69787200	Strong transcription	Primary T cells from cord blood	blood
23	chr16:69785200-69787200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr16:69785200-69787200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr16:69785200-69787200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr16:69785200-69787200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr16:69785200-69787400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr16:69785200-69787400	Weak transcription	Fetal Kidney	kidney
29	chr16:69785200-69788000	Weak transcription	Spleen	Spleen
30	chr16:69785200-69788200	Weak transcription	Gastric	stomach
31	chr16:69785600-69787200	Weak transcription	Brain Anterior Caudate	brain
32	chr16:69785600-69787200	Weak transcription	Colon Smooth Muscle	Colon
33	chr16:69785600-69787400	Weak transcription	Brain Germinal Matrix	brain
34	chr16:69785800-69787200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr16:69785800-69787200	Weak transcription	Fetal Lung	lung
36	chr16:69785800-69787200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr16:69785800-69787600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr16:69785800-69787800	Weak transcription	Lung	lung
39	chr16:69785800-69788200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr16:69786000-69787600	Weak transcription	Thymus	Thymus
41	chr16:69786200-69787200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr16:69786200-69787200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr16:69786200-69787200	Weak transcription	Fetal Intestine Large	intestine
44	chr16:69786200-69787200	Weak transcription	NHDF-Ad	bronchial
45	chr16:69786200-69787600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr16:69786400-69787200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr16:69786400-69787200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr16:69786400-69787200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr16:69786400-69787200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr16:69786400-69787200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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