Variant report

Variant	rs2871011
Chromosome Location	chr15:83229542-83229543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83226594..83230690-chr15:83232358..83235260,6	K562	blood:
2	chr15:83217765..83219665-chr15:83228669..83230495,2	K562	blood:
3	chr15:83226842..83229962-chr15:83347488..83351560,3	MCF-7	breast:
4	chr15:83227977..83230021-chr15:83296257..83298165,2	K562	blood:
5	chr15:83226594..83229969-chr15:83232358..83234992,5	K562	blood:

Variant related genes	Relation type
ENSG00000214575	Chromatin interaction
ENSG00000103723	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10163167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10520565	0.82[CHB][hapmap];0.94[CHD][hapmap];0.90[ASN][1000 genomes]
rs1145172	0.93[LWK][hapmap];0.85[MKK][hapmap]
rs1145173	0.93[LWK][hapmap];0.85[MKK][hapmap]
rs12148332	0.86[AFR][1000 genomes]
rs12148608	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap]
rs1259180	0.89[AFR][1000 genomes]
rs1259183	0.92[YRI][hapmap]
rs12592022	0.88[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1267657	0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1267659	0.93[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs17158396	0.83[GIH][hapmap]
rs17841171	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs2567635	0.93[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs2567636	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs28493687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35934048	0.86[AFR][1000 genomes]
rs36109438	0.86[AFR][1000 genomes]
rs4779042	0.82[ASN][1000 genomes]
rs57181760	0.86[AFR][1000 genomes]
rs59746564	0.94[ASN][1000 genomes]
rs698500	0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs783523	0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs783526	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs783527	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs783529	0.90[YRI][hapmap]
rs783530	0.85[AFR][1000 genomes]
rs783531	0.89[AFR][1000 genomes]
rs783532	0.89[AFR][1000 genomes]
rs783540	0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs8023333	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs803687	0.83[AFR][1000 genomes]
rs803688	0.88[AFR][1000 genomes]
rs803747	0.89[AFR][1000 genomes]
rs8039549	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427965	chr15:82741381-83310525	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv428309	chr15:82741381-83310525	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv2758391	chr15:82879646-83310525	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	esv2760046	chr15:82879646-83310525	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1035899	chr15:83108446-83315731	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833071	chr15:83123646-83310510	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2871011	AP3B2	cis	lung	GTEx
rs2871011	RP11-152F13.7	cis	Esophagus Mucosa	GTEx
rs2871011	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2871011	ST20	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83216800-83235000	Weak transcription	NHLF	lung
2	chr15:83219000-83239400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:83219800-83239800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:83222000-83235200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:83222000-83239200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:83222200-83237800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:83222600-83239400	Weak transcription	Fetal Stomach	stomach
8	chr15:83222600-83239600	Weak transcription	Ovary	ovary
9	chr15:83222600-83239600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:83222800-83240600	Weak transcription	Aorta	Aorta
11	chr15:83223400-83230200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:83223800-83233800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:83223800-83239600	Weak transcription	Brain Substantia Nigra	brain
14	chr15:83224800-83232600	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:83224800-83233400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:83224800-83233800	Weak transcription	Brain Anterior Caudate	brain
17	chr15:83224800-83235400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:83224800-83239800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:83226000-83233400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:83226600-83232200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:83227000-83233400	Weak transcription	Brain Angular Gyrus	brain
22	chr15:83227600-83232400	Weak transcription	K562	blood
23	chr15:83227800-83231200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:83229400-83230600	Enhancers	Brain Inferior Temporal Lobe	brain

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