Variant report

Variant	rs999420
Chromosome Location	chr11:17804998-17804999
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	chr11:17804443..17806483-chr11:17873609..17875464,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10160556	0.89[ASN][1000 genomes]
rs10766440	0.89[ASN][1000 genomes]
rs10832860	0.89[ASN][1000 genomes]
rs1236206	0.89[ASN][1000 genomes]
rs2079227	0.92[ASW][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2237950	0.85[ASW][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2237952	0.85[ASN][1000 genomes]
rs2283250	0.92[ASW][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2283251	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2299634	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3802969	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3802970	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4757589	0.89[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[ASN][1000 genomes]
rs7110010	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[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
rs999420	SOX6	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

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	chr11:17797800-17808600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:17798000-17819800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:17801600-17821800	Weak transcription	Spleen	Spleen
9	chr11:17802000-17805000	Enhancers	Fetal Brain Male	brain
10	chr11:17802600-17819400	Weak transcription	Esophagus	oesophagus
11	chr11:17802800-17807600	Weak transcription	Brain Angular Gyrus	brain
12	chr11:17802800-17832400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr11:17803200-17808000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:17803400-17815200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:17803400-17819400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:17804000-17809200	Weak transcription	HepG2	liver
17	chr11:17804000-17819400	Weak transcription	Liver	Liver
18	chr11:17804600-17807600	Weak transcription	Fetal Brain Female	brain
19	chr11:17804800-17809400	Weak transcription	Ovary	ovary
20	chr11:17804800-17813800	Weak transcription	Pancreas	Pancrea

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