Variant report

Variant	rs10791889
Chromosome Location	chr11:66493825-66493826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10160758	0.85[ASW][hapmap];0.86[CEU][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs10750790	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10791890	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10791891	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10791892	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10896135	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10896139	0.95[CEU][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs11227610	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs11600959	0.93[ASW][hapmap];0.90[CEU][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2077432	1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2167457	0.86[ASW][hapmap];0.95[CEU][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs2187041	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2242663	0.86[ASW][hapmap];0.80[MEX][hapmap]
rs3741194	0.95[CEU][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap]
rs3741364	1.00[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs4576826	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4930184	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4930390	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs551708	0.83[CEU][hapmap]
rs6591222	0.95[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7103627	0.86[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap]
rs7119426	0.95[CEU][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs7120256	0.95[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs714766	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7570	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs7930203	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7948839	0.90[CEU][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv897791	chr11:66442855-66533469	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv427891	chr11:66456140-66606701	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv897792	chr11:66486143-66529101	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv897793	chr11:66486143-66533469	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10791889	CTSF	cis	lymphoblastoid	seeQTL
rs10791889	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs10791889	B3GNT1	cis	parietal	SCAN
rs10791889	EHBP1L1	cis	cerebellum	SCAN
rs10791889	CTSF	cis	Whole Blood	GTEx
rs10791889	VEGFB	cis	cerebellum	SCAN
rs10791889	C11orf80	cis	cerebellum	SCAN
rs10791889	KDM2A	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66456400-66494600	Weak transcription	Right Atrium	heart
2	chr11:66482600-66494600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:66488400-66494600	Weak transcription	Brain Angular Gyrus	brain
4	chr11:66488800-66494200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:66489000-66494200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:66489000-66494400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:66489200-66494600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:66489200-66494600	Weak transcription	Spleen	Spleen
9	chr11:66489800-66494000	Weak transcription	Esophagus	oesophagus
10	chr11:66490600-66494600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:66490600-66494600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:66491000-66494000	Weak transcription	Pancreas	Pancrea
13	chr11:66491000-66494600	Weak transcription	Ovary	ovary
14	chr11:66492200-66494000	Weak transcription	A549	lung
15	chr11:66492600-66494000	Weak transcription	HMEC	breast
16	chr11:66492600-66494400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:66492600-66495000	Flanking Active TSS	Liver	Liver
18	chr11:66492800-66494600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:66492800-66494600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:66493000-66494200	Weak transcription	NHEK	skin
21	chr11:66493200-66494000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:66493200-66494200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
23	chr11:66493200-66494600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:66493200-66496000	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr11:66493400-66494000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:66493400-66494200	Enhancers	Brain Germinal Matrix	brain
27	chr11:66493400-66494200	Enhancers	Gastric	stomach
28	chr11:66493400-66494400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:66493400-66494600	Enhancers	Fetal Brain Male	brain
30	chr11:66493400-66494800	Flanking Active TSS	Fetal Brain Female	brain
31	chr11:66493400-66495200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:66493600-66494600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr11:66493800-66494000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:66493800-66494000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
35	chr11:66493800-66494000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
36	chr11:66493800-66494000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
37	chr11:66493800-66494000	Enhancers	Lung	lung
38	chr11:66493800-66494000	Enhancers	K562	blood
39	chr11:66493800-66494200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
40	chr11:66493800-66494200	Bivalent Enhancer	Stomach Mucosa	stomach
41	chr11:66493800-66494400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:66493800-66494400	Bivalent Enhancer	Fetal Muscle Leg	muscle
43	chr11:66493800-66494600	Enhancers	Brain Anterior Caudate	brain
44	chr11:66493800-66494600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
45	chr11:66493800-66494800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:66493800-66494800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
47	chr11:66493800-66494800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
48	chr11:66493800-66494800	Flanking Active TSS	Hela-S3	cervix
49	chr11:66493800-66495000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell

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