Variant report

Variant	rs4148638
Chromosome Location	chr11:17422955-17422956
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1002227	0.89[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs10466382	0.83[CEU][hapmap]
rs10766383	0.83[CEU][hapmap]
rs10766384	0.83[CEU][hapmap]
rs10766385	0.83[CEU][hapmap]
rs10766389	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs10766391	0.84[CEU][hapmap]
rs10766392	0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs10766393	0.89[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs10766396	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10832757	0.83[CEU][hapmap]
rs10832765	0.82[CEU][hapmap]
rs10832768	0.83[CEU][hapmap]
rs10832770	0.85[YRI][hapmap]
rs10832779	0.84[CEU][hapmap]
rs10832785	0.82[JPT][hapmap]
rs11024273	1.00[CEU][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes]
rs11024275	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2067043	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2074312	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074313	0.94[EUR][1000 genomes]
rs2285676	0.82[JPT][hapmap]
rs3741203	0.89[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs41282912	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5218	0.89[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9633836	0.84[CEU][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs9645621	0.83[CEU][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	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv517772	chr11:17401134-17427862	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv528959	chr11:17403639-17435214	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv467713	chr11:17408025-17440473	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv553584	chr11:17408025-17440473	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4148638	RP1-239B22.5	cis	Esophagus Mucosa	GTEx
rs4148638	NCR3LG1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17411800-17426000	Weak transcription	Lung	lung
2	chr11:17411800-17426000	Weak transcription	Pancreas	Pancrea
3	chr11:17411800-17426800	Weak transcription	Brain Hippocampus Middle	brain
4	chr11:17411800-17426800	Weak transcription	Brain Substantia Nigra	brain
5	chr11:17411800-17435000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:17413200-17432400	Weak transcription	Dnd41	blood
7	chr11:17416200-17423800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:17417800-17428200	Weak transcription	Gastric	stomach
9	chr11:17418600-17453600	Weak transcription	Fetal Brain Female	brain
10	chr11:17420000-17427000	Weak transcription	Brain Germinal Matrix	brain
11	chr11:17420600-17427000	Weak transcription	Hela-S3	cervix
12	chr11:17421000-17423600	Enhancers	Primary B cells from peripheral blood	blood
13	chr11:17421000-17424600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr11:17421400-17423000	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr11:17421400-17423400	Enhancers	HSMMtube	muscle
16	chr11:17421600-17423600	Enhancers	Fetal Muscle Leg	muscle
17	chr11:17421600-17427000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:17421800-17424400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr11:17422000-17427800	Weak transcription	Brain Angular Gyrus	brain
20	chr11:17422000-17428600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:17422000-17435800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:17422400-17423200	Enhancers	GM12878-XiMat	blood
23	chr11:17422600-17423000	Enhancers	Fetal Muscle Trunk	muscle
24	chr11:17422600-17423400	Enhancers	Right Atrium	heart
25	chr11:17422600-17427600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:17422800-17423000	Enhancers	Spleen	Spleen
27	chr11:17422800-17423400	Enhancers	Psoas Muscle	Psoas
28	chr11:17422800-17423400	Enhancers	HSMM	muscle
29	chr11:17422800-17423600	Enhancers	Left Ventricle	heart
30	chr11:17422800-17423800	Strong transcription	Brain Anterior Caudate	brain

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