Variant report

Variant	rs11772334
Chromosome Location	chr7:101149485-101149486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11760789	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11761608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11763096	1.00[CEU][hapmap]
rs11766744	1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.85[ASN][1000 genomes]
rs11770737	0.85[CEU][hapmap]
rs11771275	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773600	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12531666	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12537163	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12538381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13223538	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13245946	0.90[GIH][hapmap]
rs1476652	0.82[CHB][hapmap]
rs1476654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1558011	0.85[CHB][hapmap]
rs17135512	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17135557	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34215350	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34707022	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34942414	0.85[ASN][1000 genomes]
rs35029113	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35422294	0.82[ASN][1000 genomes]
rs35625019	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35644513	0.85[ASN][1000 genomes]
rs35905227	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67232716	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6970490	0.82[ASN][1000 genomes]
rs73180860	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7803909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs877702	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9969330	0.85[CHB][hapmap]
rs9969331	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv1030604	chr7:100717732-101223465	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv429788	chr7:100799565-101178565	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	54 gene(s)	inside rSNPs	diseases
4	nsv1017707	chr7:100968363-101156017	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1020456	chr7:100968363-101156056	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv464660	chr7:100968363-101171028	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv607981	chr7:100968363-101171028	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1021187	chr7:100993420-101178831	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv888821	chr7:101091470-101311540	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv831078	chr7:101094945-101257486	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv888822	chr7:101105017-101330734	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv888823	chr7:101109073-101174965	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv888824	chr7:101109073-101330734	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv1025029	chr7:101120515-101156998	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11772334	PDAP1	cis	parietal	SCAN
rs11772334	GATS	cis	parietal	SCAN
rs11772334	ZNF655	cis	parietal	SCAN
rs11772334	BUD31	cis	cerebellum	SCAN
rs11772334	ARMC10	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101126800-101165000	Weak transcription	Right Atrium	heart
2	chr7:101142000-101150600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:101142400-101150800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr7:101146600-101150800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:101146800-101150600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:101147400-101150600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr7:101147400-101150600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:101147400-101150600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:101148000-101150000	Weak transcription	GM12878-XiMat	blood
10	chr7:101148000-101150600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:101148000-101150600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr7:101148000-101150600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:101148000-101150800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:101148600-101150200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:101148600-101150600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:101148600-101150600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:101148600-101150600	Weak transcription	Primary B cells from cord blood	blood
18	chr7:101148800-101150800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr7:101148800-101150800	Weak transcription	Fetal Kidney	kidney
20	chr7:101149000-101150600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:101149200-101149600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr7:101149200-101151600	Enhancers	HepG2	liver
23	chr7:101149400-101149600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:101149400-101149600	Enhancers	A549	lung
25	chr7:101149400-101150000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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