Variant report

Variant	rs11024408
Chromosome Location	chr11:17823296-17823297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
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	0.89[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.83[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	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024400	0.89[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024402	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024405	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11024406	1.00[ASN][1000 genomes]
rs11024409	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12290375	1.00[ASN][1000 genomes]
rs12361234	0.86[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1236205	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1236207	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422210	1.00[ASN][1000 genomes]
rs1528	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]
rs2107428	0.91[AFR][1000 genomes];0.84[AMR][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:5 , 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	nsv526501	chr11:17816412-17824372	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11024408	SOX6	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17796800-17828800	Weak transcription	Brain Germinal Matrix	brain
2	chr11:17802800-17832400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:17805800-17829000	Weak transcription	Fetal Stomach	stomach
4	chr11:17806000-17837800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:17806800-17867400	Weak transcription	Primary B cells from cord blood	blood
6	chr11:17808200-17861400	Weak transcription	Thymus	Thymus
7	chr11:17808800-17828600	Weak transcription	Fetal Brain Female	brain
8	chr11:17808800-17834600	Weak transcription	Aorta	Aorta
9	chr11:17809000-17833200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:17809200-17824800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:17809600-17823600	Weak transcription	HSMMtube	muscle
12	chr11:17810400-17829400	Weak transcription	Fetal Intestine Small	intestine
13	chr11:17811000-17830800	Weak transcription	Primary T cells from cord blood	blood
14	chr11:17815600-17841400	Weak transcription	HepG2	liver
15	chr11:17818600-17843200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:17819200-17823800	Enhancers	Fetal Heart	heart
17	chr11:17820600-17823800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:17820600-17825200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:17820600-17825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:17820800-17832600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:17821000-17823400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:17821000-17823600	Weak transcription	NHEK	skin
23	chr11:17821200-17823800	Weak transcription	Fetal Muscle Leg	muscle
24	chr11:17821200-17826800	Weak transcription	Right Atrium	heart
25	chr11:17821200-17828200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:17821200-17831800	Weak transcription	Esophagus	oesophagus
27	chr11:17822200-17823400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:17822400-17823400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr11:17822400-17823600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr11:17822400-17826600	Weak transcription	Left Ventricle	heart
31	chr11:17822400-17826800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr11:17822400-17827000	Weak transcription	Psoas Muscle	Psoas
33	chr11:17822400-17827000	Weak transcription	Right Ventricle	heart
34	chr11:17822800-17823400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:17822800-17823600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr11:17822800-17823800	Enhancers	H9 Cell Line	embryonic stem cell
37	chr11:17823000-17823600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr11:17823000-17824000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr11:17823000-17824000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr11:17823000-17824200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:17823000-17824200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr11:17823000-17824200	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr11:17823000-17824400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr11:17823200-17823600	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr11:17823200-17824000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:17823200-17824200	Enhancers	H1 Cell Line	embryonic stem cell
47	chr11:17823200-17825600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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