Variant report

Variant	rs1463591
Chromosome Location	chr12:56170893-56170894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56135845..56138090-chr12:56170283..56173166,2	MCF-7	breast:
2	chr12:56145012..56148000-chr12:56170304..56172255,2	MCF-7	breast:
3	chr12:56123432..56125998-chr12:56170445..56172889,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135414	Chromatin interaction
ENSG00000135404	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12308277	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12320132	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17118032	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2231462	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2231464	1.00[CEU][hapmap]
rs3138140	0.82[TSI][hapmap]
rs3802998	1.00[CHB][hapmap]
rs4457792	0.82[CEU][hapmap]
rs56699787	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58599597	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59980563	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68101940	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310164	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73119263	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959622	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1463591	RDH5	cis	lymphoblastoid	seeQTL
rs1463591	BLOC1S1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56139400-56174600	Weak transcription	Stomach Mucosa	stomach
2	chr12:56142000-56191800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:56144600-56208800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:56144800-56198600	Strong transcription	Primary B cells from peripheral blood	blood
5	chr12:56145200-56199400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr12:56149400-56209600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:56152000-56173200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:56152600-56171400	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:56152600-56179600	Weak transcription	Pancreas	Pancrea
10	chr12:56152800-56209000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:56153000-56174600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:56153000-56176400	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:56153000-56182400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:56153200-56171600	Weak transcription	Esophagus	oesophagus
15	chr12:56153400-56175800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:56154400-56178400	Weak transcription	Fetal Brain Male	brain
17	chr12:56154400-56180600	Weak transcription	Right Ventricle	heart
18	chr12:56155800-56174200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:56160000-56175600	Weak transcription	Spleen	Spleen
20	chr12:56160000-56179600	Weak transcription	Aorta	Aorta
21	chr12:56160000-56197600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:56160200-56180000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:56160200-56184600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:56160400-56174800	Weak transcription	NHLF	lung
25	chr12:56160400-56209600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:56160800-56174800	Weak transcription	Lung	lung
27	chr12:56161000-56174800	Weak transcription	Brain Germinal Matrix	brain
28	chr12:56162200-56183200	Strong transcription	Primary T cells from cord blood	blood
29	chr12:56162400-56173400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:56163000-56174400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:56163000-56198600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:56163200-56175000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:56163200-56199800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:56163200-56209400	Strong transcription	Fetal Thymus	thymus
35	chr12:56163400-56184600	Strong transcription	Placenta	Placenta
36	chr12:56163400-56198000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:56163800-56177200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:56164000-56197600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:56164200-56178200	Strong transcription	Fetal Stomach	stomach
40	chr12:56164800-56185000	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:56165800-56171600	Weak transcription	Fetal Lung	lung
42	chr12:56166000-56175200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr12:56166000-56178000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:56166200-56174800	Weak transcription	Colonic Mucosa	Colon
45	chr12:56166400-56171400	Weak transcription	Brain Anterior Caudate	brain
46	chr12:56166400-56171400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr12:56166400-56171400	Weak transcription	NHDF-Ad	bronchial
48	chr12:56166400-56171600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:56166400-56171600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:56166400-56172800	Weak transcription	Primary hematopoietic stem cells	blood

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