Variant report

Variant	rs10739940
Chromosome Location	chr9:95746460-95746461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95744507..95747360-chr9:95750258..95753715,3	MCF-7	breast:
2	chr9:95735773..95738938-chr9:95746079..95753670,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127084	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10121856	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10283714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10761189	0.95[JPT][hapmap]
rs10821046	0.90[GIH][hapmap]
rs10821048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10821049	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821050	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992561	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992562	0.81[AMR][1000 genomes]
rs10992564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs11788120	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13300085	0.95[JPT][hapmap]
rs3802381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3936099	0.90[GIH][hapmap]
rs4302906	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4744159	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744161	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479445	0.95[JPT][hapmap]
rs7026624	0.95[GIH][hapmap]
rs7030160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7032953	0.83[EUR][1000 genomes]
rs7847879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7848528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850247	0.82[CEU][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs7867742	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7869056	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7869421	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7870077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7875497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9942903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9942965	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10739940	ZNF484	cis	parietal	SCAN
rs10739940	ZNF484	cis	cerebellum	SCAN
rs10739940	SUSD3	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95735400-95752600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
2	chr9:95740000-95754800	Weak transcription	Gastric	stomach
3	chr9:95740000-95754800	Weak transcription	Pancreas	Pancrea
4	chr9:95740200-95750000	Weak transcription	Esophagus	oesophagus
5	chr9:95740200-95750600	Weak transcription	Lung	lung
6	chr9:95743000-95747600	ZNF genes & repeats	Dnd41	blood
7	chr9:95743800-95748200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr9:95744400-95747600	ZNF genes & repeats	Primary B cells from cord blood	blood
9	chr9:95744400-95747600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:95744400-95747600	ZNF genes & repeats	GM12878-XiMat	blood
11	chr9:95744400-95751400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr9:95744600-95747400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr9:95744600-95749200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr9:95745200-95746800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr9:95745400-95747000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr9:95745800-95746600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr9:95745800-95746600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr9:95745800-95747200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr9:95745800-95749800	Strong transcription	Fetal Thymus	thymus
20	chr9:95745800-95753200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr9:95746000-95747000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
22	chr9:95746000-95748200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:95746200-95746600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr9:95746200-95746600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr9:95746200-95746800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:95746200-95746800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
27	chr9:95746200-95747400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr9:95746200-95747400	ZNF genes & repeats	Thymus	Thymus
29	chr9:95746200-95747800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
30	chr9:95746200-95748200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr9:95746200-95751400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr9:95746400-95747400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:95746400-95751000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:95746400-95752600	Genic enhancers	Primary T cells from cord blood	blood

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