Variant report

Variant	rs12324877
Chromosome Location	chr15:83221809-83221810
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83220388..83222174-chr15:83223442..83225725,3	MCF-7	breast:
2	chr15:83220707..83222266-chr15:83225159..83227299,2	K562	blood:
3	chr15:83213257..83215653-chr15:83219949..83222640,2	K562	blood:
4	chr15:83216641..83218294-chr15:83221044..83223302,2	K562	blood:
5	chr15:83217723..83220183-chr15:83220219..83222791,2	K562	blood:

Variant related genes	Relation type
ENSG00000214575	Chromatin interaction
ENSG00000260836	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10152286	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10163167	0.86[YRI][hapmap]
rs10468216	0.92[AFR][1000 genomes]
rs10468219	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11635460	0.91[LWK][hapmap]
rs12437576	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12438371	0.90[ASW][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs12438565	1.00[CEU][hapmap]
rs12440776	1.00[CEU][hapmap]
rs12441668	0.88[AFR][1000 genomes]
rs12441776	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442733	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs12443184	1.00[CEU][hapmap]
rs1267658	0.86[YRI][hapmap]
rs13379712	1.00[CEU][hapmap]
rs17158391	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17158405	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1877242	0.91[LWK][hapmap]
rs28485966	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4779032	0.86[YRI][hapmap]
rs55844519	0.90[AFR][1000 genomes]
rs7163990	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7182320	0.91[LWK][hapmap]
rs72751665	0.83[AFR][1000 genomes]
rs783543	0.86[YRI][hapmap]
rs9630495	0.88[AFR][1000 genomes]
rs9806591	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv428645	chr15:83069951-83227151	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	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
7	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12324877	LOC283726	cis	multi-tissue	Pritchard
rs12324877	DKFZp666G057	cis	multi-tissue	Pritchard
rs12324877	FAM154B	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83214000-83224800	Strong transcription	Stomach Smooth Muscle	stomach
2	chr15:83214200-83222600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr15:83214600-83226800	Weak transcription	Gastric	stomach
4	chr15:83216200-83222400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:83216800-83222400	Weak transcription	NHDF-Ad	bronchial
6	chr15:83216800-83222600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:83216800-83235000	Weak transcription	NHLF	lung
8	chr15:83217000-83222000	Strong transcription	Brain Cingulate Gyrus	brain
9	chr15:83217000-83222000	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr15:83217200-83222000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:83218200-83224800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:83218400-83222200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:83218600-83222000	Weak transcription	Aorta	Aorta
14	chr15:83218600-83224800	Weak transcription	Fetal Lung	lung
15	chr15:83219000-83239400	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:83219200-83222000	Enhancers	HMEC	breast
17	chr15:83219400-83222200	Strong transcription	K562	blood
18	chr15:83219400-83222600	Weak transcription	Osteobl	bone
19	chr15:83219800-83225800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr15:83219800-83239800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:83220600-83223800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr15:83221000-83222000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:83221000-83222200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:83221000-83222600	Strong transcription	Ovary	ovary
25	chr15:83221000-83222600	Weak transcription	HSMMtube	muscle
26	chr15:83221000-83223000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:83221200-83222200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:83221200-83222600	Strong transcription	Fetal Stomach	stomach
29	chr15:83221200-83222600	Strong transcription	Rectal Smooth Muscle	rectum
30	chr15:83221200-83222800	Enhancers	Psoas Muscle	Psoas
31	chr15:83221400-83222000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr15:83221400-83222000	Enhancers	Spleen	Spleen
33	chr15:83221400-83222400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:83221400-83222600	Weak transcription	NHEK	skin
35	chr15:83221400-83223200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:83221600-83222600	Genic enhancers	Brain Substantia Nigra	brain
37	chr15:83221600-83222800	Genic enhancers	Brain Anterior Caudate	brain
38	chr15:83221600-83223800	Genic enhancers	Brain Angular Gyrus	brain
39	chr15:83221800-83222200	Genic enhancers	Brain Hippocampus Middle	brain
40	chr15:83221800-83222600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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