Variant report

Variant	rs6486399
Chromosome Location	chr11:17851342-17851343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1005008	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10466421	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11024415	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11821847	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1548528	0.81[CHB][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2079227	0.81[GIH][hapmap]
rs2107427	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2158396	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237943	0.81[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2237944	0.81[CHB][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2237946	0.81[CHB][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2237948	0.88[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2237950	0.81[GIH][hapmap]
rs4757591	0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs4757593	0.81[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6486398	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7106840	0.88[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs7115183	0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7124199	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs718439	0.88[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs765989	0.81[CHB][hapmap];0.88[AMR][1000 genomes]
rs7929668	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7932686	0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7935967	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][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	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
2	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
3	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
4	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6486399	C11orf58	cis	parietal	SCAN
rs6486399	SOX6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17806800-17867400	Weak transcription	Primary B cells from cord blood	blood
2	chr11:17808200-17861400	Weak transcription	Thymus	Thymus
3	chr11:17833800-17867400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr11:17835000-17869400	Weak transcription	Fetal Intestine Small	intestine
5	chr11:17835200-17884200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:17838400-17971600	Weak transcription	Gastric	stomach
7	chr11:17838800-17860800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:17844400-17852200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr11:17844800-17862000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:17847600-17852000	Weak transcription	Spleen	Spleen
11	chr11:17848600-17853000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr11:17849000-17851800	Enhancers	Fetal Stomach	stomach
13	chr11:17849200-17852000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:17850400-17851400	Weak transcription	Psoas Muscle	Psoas
15	chr11:17850400-17852800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:17850400-17866200	Weak transcription	Aorta	Aorta
17	chr11:17850600-17851600	Weak transcription	Ovary	ovary
18	chr11:17851000-17851800	Enhancers	Fetal Kidney	kidney
19	chr11:17851200-17851800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:17851200-17867000	Weak transcription	Primary T cells from cord blood	blood

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