Variant report

Variant	rs4788449
Chromosome Location	chr16:71931219-71931220
allele	A/G
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	chr16:71931195-71931586	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:71841145..71844669-chr16:71927071..71931411,13	MCF-7	breast:
2	chr16:71878320..71880402-chr16:71929242..71933378,4	MCF-7	breast:
3	chr16:71929970..71932998-chr16:71952269..71954857,3	K562	blood:
4	chr16:71916766..71921844-chr16:71926616..71932994,12	K562	blood:
5	chr16:71928144..71931559-chr16:72041567..72044276,4	MCF-7	breast:
6	chr16:71929035..71931345-chr16:71958752..71961424,2	K562	blood:

No data

Variant related genes	Relation type
ZNF821	TF binding region
ENSG00000102967	Chromatin interaction
ENSG00000102984	Chromatin interaction
ENSG00000224470	Chromatin interaction
ENSG00000182149	Chromatin interaction
ENSG00000166747	Chromatin interaction
ENSG00000261337	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11075908	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075911	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11648353	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11648530	0.91[EUR][1000 genomes]
rs11649672	0.97[EUR][1000 genomes]
rs11859903	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12102548	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12444829	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12447045	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12449139	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12599192	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12921084	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12926041	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12926300	0.93[EUR][1000 genomes]
rs12930744	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12935795	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13329779	1.00[EUR][1000 genomes]
rs1834034	0.91[EUR][1000 genomes]
rs1834035	0.95[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs1981874	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008675	0.88[EUR][1000 genomes]
rs2018384	0.97[EUR][1000 genomes]
rs2288029	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288031	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335709	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2335710	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335711	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335712	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2335713	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335714	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335715	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28697038	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2878492	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3794692	0.98[EUR][1000 genomes]
rs4788446	0.81[EUR][1000 genomes]
rs4788447	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788450	0.92[YRI][hapmap]
rs4788562	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4788563	0.85[EUR][1000 genomes]
rs4788564	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788566	0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788570	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788571	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788573	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788576	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788579	0.92[YRI][hapmap]
rs4788581	0.97[EUR][1000 genomes]
rs4788582	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4788584	0.91[EUR][1000 genomes]
rs4788585	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs62053803	0.91[EUR][1000 genomes]
rs6499533	1.00[JPT][hapmap]
rs6499542	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6499545	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6499551	0.99[EUR][1000 genomes]
rs6499552	1.00[EUR][1000 genomes]
rs6558	1.00[JPT][hapmap]
rs7184437	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7184486	0.92[CEU][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7187129	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7193731	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7194858	1.00[JPT][hapmap]
rs7204708	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs7205154	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8044342	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8046859	0.93[EUR][1000 genomes]
rs8050488	0.89[EUR][1000 genomes]
rs8050651	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8051038	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8054111	0.88[EUR][1000 genomes]
rs8054175	0.88[EUR][1000 genomes]
rs8054403	0.87[EUR][1000 genomes]
rs8057124	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs8058118	0.98[EUR][1000 genomes]
rs8059053	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8062946	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8063324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8063403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9302631	1.00[EUR][1000 genomes]
rs9302632	0.99[EUR][1000 genomes]
rs9806882	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9806905	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9888748	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9889011	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9921412	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9932922	0.87[EUR][1000 genomes]
rs9934803	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9934812	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9937936	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised 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 miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS 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	89 gene(s)	inside rSNPs	diseases
3	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv906893	chr16:71922663-71988728	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4788449	PSMD7	cis	parietal	SCAN
rs4788449	SNTB2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71927800-71931400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr16:71927800-71931400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr16:71928000-71932000	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr16:71928200-71931400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr16:71928200-71931400	Active TSS	GM12878-XiMat	blood
6	chr16:71929600-71931600	Active TSS	Right Atrium	heart
7	chr16:71930000-71931600	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr16:71930000-71931600	Active TSS	Fetal Brain Female	brain
9	chr16:71930400-71931600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr16:71930400-71932200	Enhancers	Spleen	Spleen
11	chr16:71930400-71934800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr16:71930600-71931600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr16:71930600-71932400	Enhancers	Aorta	Aorta
14	chr16:71930600-71934200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr16:71930800-71931400	Enhancers	Brain Anterior Caudate	brain
16	chr16:71930800-71931400	Enhancers	Fetal Kidney	kidney
17	chr16:71930800-71931400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr16:71930800-71931600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr16:71930800-71931600	Enhancers	Liver	Liver
20	chr16:71930800-71931600	Enhancers	Fetal Brain Male	brain
21	chr16:71930800-71931600	Weak transcription	Pancreas	Pancrea
22	chr16:71930800-71932200	Weak transcription	Gastric	stomach
23	chr16:71930800-71932400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr16:71930800-71932400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr16:71930800-71933400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr16:71930800-71933600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr16:71930800-71934000	Enhancers	Ovary	ovary
28	chr16:71930800-71934400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr16:71930800-71934800	Enhancers	Small Intestine	intestine
30	chr16:71930800-71935400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr16:71930800-71935400	Enhancers	Primary T cells fromperipheralblood	blood
32	chr16:71930800-71943200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr16:71930800-71944200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr16:71930800-71950000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr16:71930800-71951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr16:71931000-71931400	Enhancers	Thymus	Thymus
37	chr16:71931000-71931800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr16:71931000-71932000	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr16:71931000-71934000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr16:71931000-71934600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:71931000-71934600	Enhancers	Colon Smooth Muscle	Colon
42	chr16:71931000-71937000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr16:71931000-71937800	Enhancers	Primary B cells from peripheral blood	blood
44	chr16:71931000-71942800	Weak transcription	Fetal Heart	heart
45	chr16:71931000-71949400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr16:71931000-71949600	Weak transcription	NHEK	skin
47	chr16:71931200-71931400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr16:71931200-71931400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
49	chr16:71931200-71931400	Enhancers	Primary B cells from cord blood	blood
50	chr16:71931200-71931400	Enhancers	Primary hematopoietic stem cells	blood

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