Variant report

Variant	rs12900374
Chromosome Location	chr15:83410013-83410014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:83409972-83410022	GM12891	blood:	n/a
2	chr15:83409972-83410022	HAEpiC	amniotic membrane:	n/a
3	chr15:83409972-83410022	SKMC	muscle:	n/a
4	chr15:83409972-83410022	BE2_C	brain:	n/a
5	chr15:83409972-83410022	HEK293	kidney:	embryo
6	chr15:83409972-83410022	Hela-S3	cervix:	n/a
7	chr15:83409972-83410022	AG04449	skin:	fetal
8	chr15:83409972-83410022	HCF	heart:	n/a
9	chr15:83409972-83410022	SK-N-MC	brain:	n/a
10	chr15:83409972-83410022	SAEC	small airway:	n/a
11	chr15:83409972-83410022	PrEC	prostate:	n/a
12	chr15:83409972-83410022	AoSMC	blood vessel:	n/a
13	chr15:83409972-83410022	SK-N-SH	brain:	n/a
14	chr15:83409972-83410022	NHBE	bronchial:	n/a
15	chr15:83409972-83410022	HMEC	breast:	n/a
16	chr15:83409972-83410022	HNPCEpiC	eye:	n/a
17	chr15:83409972-83410022	HRPEpiC	eye:	n/a
18	chr15:83409972-83410022	NHDF-neo	bronchial:	n/a
19	chr15:83409972-83410022	GM19239	blood:	n/a
20	chr15:83409972-83410022	ECC-1	luminal epithelium:	n/a
21	chr15:83409972-83410022	HPAEpiC	pulmonary alveolar:	n/a
22	chr15:83409972-83410022	AG09309	skin:	n/a
23	chr15:83409972-83410022	PFSK-1	brain:	n/a
24	chr15:83409972-83410022	U87	brain:	n/a
25	chr15:83409972-83410022	ovcar-3	ovarian:	n/a
26	chr15:83409972-83410022	T-47D	breast:	n/a
27	chr15:83409972-83410022	NH-A	brain:	n/a
28	chr15:83409972-83410022	GM12878	blood:	n/a
29	chr15:83409972-83410022	NB4	blood:	n/a
30	chr15:83409972-83410022	Caco-2	colon:	n/a
31	chr15:83409972-83410022	NT2-D1	testis:	n/a
32	chr15:83409972-83410022	A549	lung:	n/a
33	chr15:83409972-83410022	MCF10A-Er-Src	breast:	n/a
34	chr15:83409972-83410022	ProgFib	skin:	n/a
35	chr15:83409972-83410022	HUVEC	blood vessel:	n/a
36	chr15:83409972-83410022	Jurkat	blood:	n/a
37	chr15:83409972-83410022	Hepatocyte	liver:	n/a
38	chr15:83409972-83410022	SK-N-SH_RA	brain:	n/a
39	chr15:83409972-83410022	IMR90	lung:	fetal
40	chr15:83409972-83410022	GM06990	blood:	n/a
41	chr15:83409972-83410022	HCPEpiC	choroid plexus:	n/a
42	chr15:83409972-83410022	HRCEpiC	kidney:	n/a
43	chr15:83409972-83410022	PANC-1	pancreas:	n/a
44	chr15:83409972-83410022	RPTEC	kidney:	n/a
45	chr15:83409972-83410022	HepG2	liver:	n/a
46	chr15:83409972-83410022	AG09319	gingival:	n/a
47	chr15:83409972-83410022	BJ	skin:	n/a
48	chr15:83409972-83410022	HCM	heart:	n/a
49	chr15:83409972-83410022	AG04450	lung:	fetal
50	chr15:83409972-83410022	HRE	kidney:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83407952..83410199-chr15:83477270..83479894,2	MCF-7	breast:
2	chr15:83408600..83412115-chr15:83418405..83421158,4	K562	blood:
3	chr15:83347939..83350653-chr15:83409789..83412363,2	MCF-7	breast:
4	chr15:83409906..83413739-chr15:83417431..83421180,7	MCF-7	breast:
5	chr15:83408472..83412054-chr15:83414061..83416851,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259442	CpG island
ENSG00000259315	CpG island
ENSG00000156232	Chromatin interaction
ENSG00000103723	Chromatin interaction
ENSG00000250988	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12899020	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs12909628	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12915384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17158396	1.00[CHD][hapmap]
rs1877240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36111056	0.85[AFR][1000 genomes]
rs3850610	1.00[CHD][hapmap]
rs3914699	1.00[CHD][hapmap]
rs4617830	0.87[AFR][1000 genomes]
rs4779033	1.00[CHD][hapmap]
rs7161977	1.00[CHD][hapmap]
rs7163848	1.00[CHD][hapmap];1.00[LWK][hapmap]
rs7165690	1.00[CHD][hapmap]
rs7178859	1.00[CHD][hapmap];0.90[LWK][hapmap]
rs7496832	1.00[CHD][hapmap]
rs8040488	1.00[CHD][hapmap]

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	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	esv3413738	chr15:83390947-83422928	Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12900374	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs12900374	AP3B2	cis	multi-tissue	Pritchard
rs12900374	AP3B2	cis	Adipose Subcutaneous	GTEx
rs12900374	AP3B2	cis	Nerve Tibial	GTEx
rs12900374	WHAMM	cis	parietal	SCAN
rs12900374	BTBD1	cis	cerebellum	SCAN
rs12900374	AP3B2	cis	Thyroid	GTEx
rs12900374	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12900374	AP3B2	cis	Artery Tibial	GTEx
rs12900374	AP3B2	cis	Muscle Skeletal	GTEx
rs12900374	AP3B2	cis	lung	GTEx
rs12900374	DNAJA4	cis	parietal	SCAN
rs12900374	ARNT2	cis	cerebellum	SCAN
rs12900374	AP3B2	cis	Esophagus Muscularis	GTEx
rs12900374	ACSBG1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83393800-83418400	Weak transcription	Thymus	Thymus
2	chr15:83394400-83418200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr15:83394400-83418400	Weak transcription	Primary B cells from cord blood	blood
4	chr15:83394800-83418400	Weak transcription	Brain Angular Gyrus	brain
5	chr15:83395800-83418200	Weak transcription	GM12878-XiMat	blood
6	chr15:83396200-83417800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:83396600-83418200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:83397600-83410600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:83398400-83418200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:83399200-83418000	Weak transcription	Left Ventricle	heart
11	chr15:83399600-83410600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:83399800-83413400	Weak transcription	Lung	lung
13	chr15:83399800-83418400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:83399800-83418400	Weak transcription	Adipose Nuclei	Adipose
15	chr15:83400400-83418400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr15:83401200-83418400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr15:83401800-83410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:83402000-83418200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:83402200-83411200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:83402400-83412800	Weak transcription	Fetal Muscle Leg	muscle
21	chr15:83402400-83418200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:83402600-83418200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr15:83402800-83411200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:83402800-83418200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:83403600-83410600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:83404000-83418000	Weak transcription	Dnd41	blood
27	chr15:83404200-83410800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:83405200-83411200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:83405200-83411200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:83405200-83418400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr15:83405400-83418600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:83406400-83418200	Weak transcription	Liver	Liver
33	chr15:83406800-83418400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:83407200-83418200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr15:83407400-83418400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:83407600-83418000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:83407600-83418200	Weak transcription	Primary T cells from cord blood	blood
38	chr15:83407800-83418400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr15:83408200-83410200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:83408200-83410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:83408200-83410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:83408200-83410400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:83408600-83418200	Weak transcription	HSMM	muscle
44	chr15:83410000-83410400	Enhancers	NHEK	skin
45	chr15:83410000-83411000	Enhancers	HMEC	breast
46	chr15:83410000-83411400	Weak transcription	Placenta	Placenta

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