Variant report

Variant	rs1528
Chromosome Location	chr11:17809724-17809725
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	chr11:17802511..17804986-chr11:17809141..17810811,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SERGEF-1	chr11:17809595-17809960	NONHSAT018249
2	lnc-SERGEF-1	chr11:17809595-17809960	NONHSAT018248
3	lnc-SERGEF-1	chr11:17809599-17809960	NONHSAT018251
4	lnc-SERGEF-1	chr11:17809595-17809960	NONHSAT018250

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1012106	1.00[ASN][1000 genomes]
rs10734255	1.00[ASN][1000 genomes]
rs10766433	1.00[ASN][1000 genomes]
rs10788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832821	1.00[ASN][1000 genomes]
rs10832822	1.00[ASN][1000 genomes]
rs10832823	1.00[ASN][1000 genomes]
rs11024354	1.00[ASN][1000 genomes]
rs11024399	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024400	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024402	0.88[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024405	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11024406	1.00[ASN][1000 genomes]
rs11024408	0.89[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024409	0.90[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12290375	1.00[ASN][1000 genomes]
rs12361234	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1236205	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1236207	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422210	1.00[ASN][1000 genomes]
rs2107428	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336851	1.00[ASN][1000 genomes]
rs3858514	1.00[ASN][1000 genomes]
rs7125500	1.00[ASN][1000 genomes]
rs71484782	1.00[ASN][1000 genomes]
rs740320	1.00[ASN][1000 genomes]
rs757513	1.00[ASN][1000 genomes]
rs757515	1.00[ASN][1000 genomes]
rs757516	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467718	chr11:17744992-17809724	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv553589	chr11:17744992-17809724	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv516767	chr11:17758587-17809724	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv832078	chr11:17780503-17953521	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1043973	chr11:17781560-17869896	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1528	SOX6	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17788000-17811400	Weak transcription	Brain Anterior Caudate	brain
2	chr11:17792000-17815000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr11:17792000-17818400	Weak transcription	Right Atrium	heart
4	chr11:17793200-17809800	Weak transcription	Fetal Intestine Small	intestine
5	chr11:17796800-17828800	Weak transcription	Brain Germinal Matrix	brain
6	chr11:17798000-17819800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr11:17801600-17821800	Weak transcription	Spleen	Spleen
8	chr11:17802600-17819400	Weak transcription	Esophagus	oesophagus
9	chr11:17802800-17832400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr11:17803400-17815200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:17803400-17819400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:17804000-17819400	Weak transcription	Liver	Liver
13	chr11:17804800-17813800	Weak transcription	Pancreas	Pancrea
14	chr11:17805000-17819800	Weak transcription	Fetal Brain Male	brain
15	chr11:17805800-17829000	Weak transcription	Fetal Stomach	stomach
16	chr11:17806000-17837800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr11:17806600-17815200	Weak transcription	Lung	lung
18	chr11:17806600-17817200	Weak transcription	Gastric	stomach
19	chr11:17806600-17819400	Weak transcription	Right Ventricle	heart
20	chr11:17806800-17867400	Weak transcription	Primary B cells from cord blood	blood
21	chr11:17807200-17812400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr11:17807200-17818600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:17807400-17810400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:17807600-17810400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:17807600-17810800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:17807800-17810200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr11:17807800-17812000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:17808200-17814000	Weak transcription	Brain Angular Gyrus	brain
29	chr11:17808200-17861400	Weak transcription	Thymus	Thymus
30	chr11:17808400-17810600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:17808600-17811000	Strong transcription	Primary T cells from cord blood	blood
32	chr11:17808800-17813800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:17808800-17822200	Weak transcription	Adipose Nuclei	Adipose
34	chr11:17808800-17828600	Weak transcription	Fetal Brain Female	brain
35	chr11:17808800-17834600	Weak transcription	Aorta	Aorta
36	chr11:17809000-17809800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr11:17809000-17812200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:17809000-17813600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:17809000-17815800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:17809000-17833200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:17809200-17810000	Strong transcription	HepG2	liver
42	chr11:17809200-17812000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:17809200-17812000	Weak transcription	NHEK	skin
44	chr11:17809200-17824800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr11:17809400-17810000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:17809400-17811000	Strong transcription	Ovary	ovary
47	chr11:17809400-17812000	Weak transcription	NHDF-Ad	bronchial
48	chr11:17809400-17812400	Weak transcription	HMEC	breast
49	chr11:17809400-17819200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:17809600-17811200	Weak transcription	Rectal Mucosa Donor 29	rectum

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