Variant report

Variant	rs3781939
Chromosome Location	chr11:72292167-72292168
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr11:72292131-72292377	GM12878	blood:	n/a	chr11:72292273-72292284 chr11:72292293-72292304
2	USF2	chr11:72291984-72292190	Hela-S3	cervix:	n/a	n/a
3	EBF1	chr11:72292112-72292459	GM12878	blood:	n/a	chr11:72292273-72292284 chr11:72292293-72292304
4	CTCF	chr11:72292100-72292250	NHEK	skin:	n/a	n/a
5	EBF1	chr11:72292140-72292362	GM12878	blood:	n/a	chr11:72292273-72292284 chr11:72292293-72292304
6	CTCF	chr11:72292060-72292210	HEEpiC	esophagus:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:72290299..72292837-chr11:72306814..72308929,2	K562	blood:
2	chr11:72289408..72292307-chr11:72292834..72294829,2	MCF-7	breast:

Variant related genes	Relation type
PDE2A	TF binding region
ENSG00000256633	TF binding region
ENSG00000186642	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10793036	0.94[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs11235546	0.87[ASN][1000 genomes]
rs11235551	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs1135029	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605051	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12146545	0.80[JPT][hapmap]
rs12797791	0.83[JPT][hapmap]
rs1391888	0.80[JPT][hapmap]
rs1467135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168173	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980089	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980090	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280098	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs341049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs341086	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.88[ASN][1000 genomes]
rs341088	0.91[ASN][1000 genomes]
rs3781938	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825009	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs429075	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456405	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs458275	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs458575	0.94[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs4943939	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs56350365	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61895571	0.87[ASN][1000 genomes]
rs90409	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs907850	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794740	chr11:72021720-72332931	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
2	esv1806140	chr11:72268466-72546175	Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
3	esv1832864	chr11:72270965-72389125	Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
4	nsv832207	chr11:72272750-72469122	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
5	nsv468633	chr11:72281884-72336564	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv468634	chr11:72281884-72336564	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv555406	chr11:72281884-72336564	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
8	nsv523601	chr11:72281884-72430935	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
9	nsv468635	chr11:72284569-72336564	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv555407	chr11:72284569-72336564	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3781939	SUV420H1	cis	parietal	SCAN
rs3781939	MRPL21	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72269600-72295200	Weak transcription	Right Atrium	heart
2	chr11:72282800-72295200	Weak transcription	Gastric	stomach
3	chr11:72285000-72292200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:72285000-72296200	Weak transcription	Liver	Liver
5	chr11:72287400-72293000	Strong transcription	Fetal Muscle Leg	muscle
6	chr11:72287400-72295200	Strong transcription	Brain Hippocampus Middle	brain
7	chr11:72287400-72296600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:72287600-72293000	Strong transcription	Brain Cingulate Gyrus	brain
9	chr11:72287600-72295000	Strong transcription	Adipose Nuclei	Adipose
10	chr11:72287600-72295000	Strong transcription	Right Ventricle	heart
11	chr11:72287800-72294200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr11:72287800-72294800	Strong transcription	Fetal Brain Female	brain
13	chr11:72287800-72296400	Strong transcription	Stomach Smooth Muscle	stomach
14	chr11:72288000-72293200	Strong transcription	Brain Germinal Matrix	brain
15	chr11:72288000-72293600	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr11:72289200-72293600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
17	chr11:72289200-72294000	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:72289400-72292200	Weak transcription	Left Ventricle	heart
19	chr11:72289400-72299800	Weak transcription	Lung	lung
20	chr11:72289800-72295600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:72290800-72294600	Strong transcription	Brain Anterior Caudate	brain
22	chr11:72291000-72294800	Strong transcription	Colon Smooth Muscle	Colon
23	chr11:72291000-72295400	Weak transcription	Esophagus	oesophagus
24	chr11:72291200-72293600	Strong transcription	HSMMtube	muscle
25	chr11:72291200-72293800	Strong transcription	Brain Angular Gyrus	brain
26	chr11:72291400-72292600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:72291400-72293600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:72291600-72293400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:72291600-72295600	Strong transcription	Spleen	Spleen
30	chr11:72291800-72292600	Strong transcription	Fetal Intestine Small	intestine
31	chr11:72292000-72292400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:72292000-72295200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr11:72292000-72295800	Weak transcription	Primary B cells from cord blood	blood
34	chr11:72292000-72296000	Weak transcription	Hela-S3	cervix

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