Variant report

Variant	rs11780980
Chromosome Location	chr8:11282893-11282894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10108511	1.00[CHB][hapmap]
rs1042701	1.00[CHB][hapmap]
rs11250146	1.00[CHB][hapmap]
rs11775640	1.00[ASN][1000 genomes]
rs11775779	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11776159	1.00[CHB][hapmap]
rs11776834	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11777273	1.00[CHB][hapmap]
rs11778177	1.00[ASN][1000 genomes]
rs11780432	1.00[ASN][1000 genomes]
rs11781057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781400	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11784016	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11784897	1.00[ASN][1000 genomes]
rs11787413	1.00[ASN][1000 genomes]
rs12156238	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13268130	1.00[CHB][hapmap]
rs13272061	1.00[CHB][hapmap]
rs13280447	1.00[ASN][1000 genomes]
rs13281992	1.00[ASN][1000 genomes]
rs13439415	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13439487	1.00[ASN][1000 genomes]
rs1382567	1.00[CHB][hapmap]
rs1478890	1.00[CHB][hapmap]
rs17744726	1.00[CHB][hapmap]
rs2127127	1.00[CHB][hapmap]
rs2245232	1.00[CHB][hapmap]
rs2251301	1.00[CHB][hapmap]
rs2264306	1.00[CHB][hapmap]
rs2264866	1.00[CHB][hapmap]
rs2409776	1.00[ASN][1000 genomes]
rs2409777	1.00[ASN][1000 genomes]
rs2409779	1.00[ASN][1000 genomes]
rs2409784	1.00[CHB][hapmap]
rs2409798	1.00[CHB][hapmap]
rs2618434	1.00[CHB][hapmap]
rs2736342	1.00[CHB][hapmap]
rs28485693	1.00[ASN][1000 genomes]
rs28680779	1.00[ASN][1000 genomes]
rs34281672	1.00[ASN][1000 genomes]
rs34365278	1.00[ASN][1000 genomes]
rs34443092	1.00[ASN][1000 genomes]
rs34906655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35451013	1.00[ASN][1000 genomes]
rs35619722	1.00[ASN][1000 genomes]
rs35822699	1.00[ASN][1000 genomes]
rs36043848	1.00[ASN][1000 genomes]
rs4410870	1.00[CHB][hapmap]
rs4606022	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4840567	1.00[CHB][hapmap]
rs4840570	1.00[ASN][1000 genomes]
rs4841541	1.00[ASN][1000 genomes]
rs4841545	1.00[CHB][hapmap]
rs4841548	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4841567	1.00[CHB][hapmap]
rs56302795	1.00[ASN][1000 genomes]
rs57526558	1.00[ASN][1000 genomes]
rs67390008	1.00[ASN][1000 genomes]
rs6984115	1.00[ASN][1000 genomes]
rs6999912	1.00[CHB][hapmap]
rs7464263	1.00[CHB][hapmap]
rs7822109	1.00[CHB][hapmap]
rs7823274	1.00[ASN][1000 genomes]
rs7831369	1.00[ASN][1000 genomes]
rs7831885	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs936546	1.00[ASN][1000 genomes]
rs9650624	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv470183	chr8:11236975-11307118	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv465465	chr8:11245064-11307118	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv610275	chr8:11245064-11307118	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv522860	chr8:11253879-11330364	Bivalent/Poised TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv1792231	chr8:11278307-11289053	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11780980	MSRA	cis	parietal	SCAN
rs11780980	FAM167A	cis	parietal	SCAN
rs11780980	TDH	cis	cerebellum	SCAN
rs11780980	DEFB134	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11269400-11287400	Weak transcription	Right Atrium	heart
2	chr8:11271600-11291000	Weak transcription	Pancreas	Pancrea
3	chr8:11273000-11286800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:11273000-11287000	Weak transcription	NHEK	skin
5	chr8:11276600-11291200	Weak transcription	Gastric	stomach
6	chr8:11277600-11287000	Enhancers	Fetal Thymus	thymus
7	chr8:11279400-11288000	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr8:11279800-11289600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr8:11280000-11283800	Weak transcription	Thymus	Thymus
10	chr8:11280200-11283000	Enhancers	Brain Substantia Nigra	brain
11	chr8:11280200-11283400	Enhancers	Brain Cingulate Gyrus	brain
12	chr8:11280400-11283400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr8:11280400-11283800	Enhancers	Brain Hippocampus Middle	brain
14	chr8:11280600-11286000	Enhancers	H9 Cell Line	embryonic stem cell
15	chr8:11280600-11308800	Weak transcription	Primary B cells from cord blood	blood
16	chr8:11280800-11297600	Weak transcription	Spleen	Spleen
17	chr8:11281400-11284600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:11281600-11283000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr8:11281600-11284600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr8:11281600-11285800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr8:11281600-11286800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr8:11282000-11283000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr8:11282200-11283000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr8:11282200-11283200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr8:11282200-11284800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr8:11282200-11285400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr8:11282200-11286600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr8:11282200-11286800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr8:11282200-11287600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr8:11282400-11283000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr8:11282400-11284400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr8:11282400-11284600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr8:11282400-11284800	Weak transcription	Brain Angular Gyrus	brain
34	chr8:11282600-11283400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr8:11282600-11286600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr8:11282800-11283000	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr8:11282800-11283000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr8:11282800-11283000	Enhancers	Brain Anterior Caudate	brain
39	chr8:11282800-11283400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr8:11282800-11285400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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