Variant report

Variant	rs11996027
Chromosome Location	chr8:10891395-10891396
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10100449	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10101901	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10102241	1.00[JPT][hapmap]
rs10108304	1.00[CHB][hapmap]
rs10110123	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10111751	1.00[CHB][hapmap]
rs10282848	1.00[CHB][hapmap]
rs11250110	1.00[CHB][hapmap]
rs11250111	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11250120	1.00[CHB][hapmap]
rs11784312	1.00[CHB][hapmap]
rs11785788	1.00[CHB][hapmap]
rs11986748	1.00[CHB][hapmap]
rs11991121	1.00[CHB][hapmap]
rs11997616	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11998417	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12216784	1.00[CHB][hapmap]
rs12335200	0.82[ASN][1000 genomes]
rs17152785	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17152791	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17152793	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17152795	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17152862	1.00[CHB][hapmap]
rs17152881	1.00[CHB][hapmap]
rs17152921	1.00[CHB][hapmap]
rs17152930	1.00[CHB][hapmap]
rs17152938	1.00[CHB][hapmap]
rs17152978	1.00[CHB][hapmap]
rs17155406	1.00[JPT][hapmap]
rs17722940	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17725809	1.00[CHB][hapmap]
rs17726352	1.00[CHB][hapmap]
rs17779093	1.00[CHB][hapmap]
rs2001433	1.00[JPT][hapmap]
rs2409683	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2409732	1.00[CHB][hapmap]
rs2898254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2898258	1.00[CHB][hapmap]
rs35850128	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35995832	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4074356	1.00[CHB][hapmap]
rs4076425	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs4141827	0.82[ASN][1000 genomes]
rs4270924	1.00[CHB][hapmap]
rs4349949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4370496	1.00[CHB][hapmap]
rs4386942	1.00[CHB][hapmap]
rs4841473	1.00[CHB][hapmap]
rs4841486	1.00[CHD][hapmap]
rs59008721	0.82[ASN][1000 genomes]
rs60514110	0.82[ASN][1000 genomes]
rs60680986	0.82[ASN][1000 genomes]
rs61027371	0.82[ASN][1000 genomes]
rs6601548	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6601549	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6601550	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6983680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6994928	1.00[CHB][hapmap]
rs6999969	1.00[CHB][hapmap]
rs7000298	1.00[CHB][hapmap]
rs7000431	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7010099	1.00[CHB][hapmap]
rs7010126	1.00[CHB][hapmap]
rs7014291	1.00[CHB][hapmap]
rs7015045	1.00[JPT][hapmap]
rs7016361	1.00[CHB][hapmap]
rs7350066	1.00[CHB][hapmap]
rs7350072	1.00[CHB][hapmap]
rs73541286	0.82[ASN][1000 genomes]
rs73541293	0.82[ASN][1000 genomes]
rs73541296	0.82[ASN][1000 genomes]
rs73541300	0.82[ASN][1000 genomes]
rs73541301	0.82[ASN][1000 genomes]
rs7820231	1.00[CHB][hapmap]
rs7820777	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7822400	1.00[CHB][hapmap]
rs7833741	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7838051	1.00[CHB][hapmap]
rs7840980	1.00[CHB][hapmap]
rs7841435	1.00[CHB][hapmap]
rs7842214	1.00[CHB][hapmap]
rs7845088	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs9329237	1.00[CHB][hapmap]

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	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1022434	chr8:10866242-10916523	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	esv3438938	chr8:10888542-10893040	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	16 gene(s)	inside rSNPs	diseases
5	esv3447417	chr8:10889142-10892340	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11996027	DEFB136	cis	parietal	SCAN
rs11996027	FLJ10661	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10874400-10892800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr8:10880000-10896800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr8:10881400-10893200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr8:10883400-10899600	Weak transcription	Brain Anterior Caudate	brain
5	chr8:10884400-10892800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr8:10887800-10894800	Weak transcription	Fetal Stomach	stomach
7	chr8:10888400-10892600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr8:10889000-10891800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr8:10889800-10892200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:10889800-10894000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr8:10889800-10910800	Weak transcription	HSMMtube	muscle
12	chr8:10890200-10891800	Strong transcription	Pancreas	Pancrea
13	chr8:10890200-10891800	Strong transcription	Stomach Smooth Muscle	stomach
14	chr8:10890400-10892200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr8:10890400-10894000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr8:10890400-10895600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr8:10890400-10896800	Weak transcription	Spleen	Spleen
18	chr8:10890800-10892600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr8:10890800-10894800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr8:10891000-10891600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr8:10891000-10892800	Weak transcription	Brain Angular Gyrus	brain
22	chr8:10891000-10893200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:10891000-10893800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr8:10891000-10894000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr8:10891200-10892000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr8:10891200-10892400	Weak transcription	Gastric	stomach
27	chr8:10891200-10894400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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