Variant report

Variant	rs10796268
Chromosome Location	chr10:6603917-6603918
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10752351	1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10752356	1.00[ASW][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10752357	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10796257	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10906828	0.94[AMR][1000 genomes]
rs11259486	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1327245	0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1327246	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1327247	0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1541032	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1887325	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1983910	0.95[AMR][1000 genomes]
rs1998939	0.82[ASW][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1998940	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2011261	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4748138	1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4750596	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4750617	0.80[EUR][1000 genomes]
rs6602825	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7069738	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7916556	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7916931	0.93[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs943446	0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs943448	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9645607	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1047309	chr10:6495583-6714060	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv549912	chr10:6566975-6629225	Enhancers Active TSS Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS 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	15 gene(s)	inside rSNPs	diseases
4	esv3352661	chr10:6603858-6604054	Enhancers Weak transcription Flanking Active TSS Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10796268	STAT1	trans	brain	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6587800-6604200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:6595400-6605000	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr10:6598000-6604000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr10:6598000-6605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr10:6598000-6605200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:6598000-6605200	Weak transcription	Lung	lung
7	chr10:6598000-6605800	Weak transcription	Spleen	Spleen
8	chr10:6598000-6608000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:6598000-6612000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr10:6598600-6606800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:6601000-6604200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr10:6601000-6605200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr10:6601200-6604800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr10:6601400-6604000	Weak transcription	Thymus	Thymus
15	chr10:6601400-6605000	Weak transcription	Psoas Muscle	Psoas
16	chr10:6602000-6604400	Genic enhancers	Fetal Thymus	thymus
17	chr10:6602200-6604000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr10:6602400-6604000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr10:6602400-6604200	Weak transcription	Dnd41	blood
20	chr10:6602400-6604600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr10:6602400-6605200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr10:6602400-6605200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr10:6602600-6604800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr10:6602600-6605000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr10:6603200-6604600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:6603200-6605000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr10:6603200-6610200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr10:6603400-6604800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr10:6603400-6605600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr10:6603600-6604000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr10:6603600-6604600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr10:6603600-6605000	Enhancers	Primary hematopoietic stem cells	blood
33	chr10:6603600-6605000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr10:6603600-6605000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr10:6603600-6605200	Enhancers	Primary T cells from cord blood	blood
36	chr10:6603600-6608400	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr10:6603600-6608800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr10:6603800-6604200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr10:6603800-6605400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr10:6603800-6606600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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