Variant report

Variant	rs12591994
Chromosome Location	chr15:75320306-75320307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:119177443..119177955-chr15:75319985..75320485,2	NB4	blood:
2	chr15:75314427..75332274-chr15:75491598..75502885,56	MCF-7	breast:
3	chr15:75314438..75320960-chr15:75334023..75339188,6	K562	blood:
4	chr15:75314704..75323577-chr15:75491522..75500562,29	MCF-7	breast:
5	chr15:75247632..75249513-chr15:75319371..75321803,2	MCF-7	breast:
6	chr15:75314737..75326433-chr15:75490770..75500610,30	K562	blood:
7	chr15:75312886..75327225-chr15:75491522..75500922,36	K562	blood:
8	chr15:75318584..75321988-chr15:75334747..75339188,4	K562	blood:
9	chr15:75319473..75322181-chr17:62205905..62208887,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000167173	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000178607	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11072519	0.87[CEU][hapmap]
rs12591175	0.82[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12592477	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12593476	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12593542	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12594117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289582	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2304904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28394281	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812946	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3816261	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3910748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55877218	0.85[ASN][1000 genomes]
rs56828495	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56970592	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58068887	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58294763	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58403754	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58645417	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59094290	0.94[ASN][1000 genomes]
rs59303424	0.82[ASN][1000 genomes]
rs61166993	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495135	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495136	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495137	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495138	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495140	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495146	0.82[ASN][1000 genomes]
rs7163390	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7166105	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7167415	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7168638	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7172065	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7172715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172989	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7173218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174129	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7177109	0.83[ASN][1000 genomes]
rs7179097	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7181942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7182286	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72475969	0.82[ASN][1000 genomes]
rs7342591	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7342601	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73432941	0.81[ASN][1000 genomes]
rs73436579	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73436586	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73438537	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73438554	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73438569	0.83[ASN][1000 genomes]
rs74023908	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74023935	0.83[ASN][1000 genomes]
rs74025863	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8031545	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8033125	0.80[ASN][1000 genomes]
rs8034149	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8036573	0.94[ASN][1000 genomes]
rs8038365	0.81[ASN][1000 genomes]
rs8039433	0.82[ASN][1000 genomes]
rs8040961	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9672926	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9672995	0.92[ASN][1000 genomes]
rs9672996	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9673012	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9788648	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv527237	chr15:75305040-75321262	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12591994	PPCDC	cis	Thyroid	GTEx
rs12591994	SCAMP5	cis	Esophagus Mucosa	GTEx
rs12591994	SCAMP5	cis	Artery Tibial	GTEx
rs12591994	PPCDC	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75316600-75321000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75316600-75321000	Weak transcription	Brain Substantia Nigra	brain
3	chr15:75316600-75321600	Enhancers	Primary hematopoietic stem cells	blood
4	chr15:75316600-75321800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:75316600-75336800	Weak transcription	Fetal Brain Female	brain
6	chr15:75316800-75320400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:75316800-75320600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:75316800-75320800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:75316800-75321000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:75316800-75321000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:75316800-75321400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:75316800-75321400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:75316800-75321400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:75316800-75321400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:75316800-75321400	Weak transcription	HUVEC	blood vessel
16	chr15:75316800-75321600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:75316800-75321600	Weak transcription	HMEC	breast
18	chr15:75316800-75321600	Weak transcription	Osteobl	bone
19	chr15:75316800-75321800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:75316800-75321800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:75316800-75321800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:75316800-75321800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:75316800-75321800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr15:75316800-75321800	Weak transcription	Esophagus	oesophagus
25	chr15:75316800-75321800	Weak transcription	Gastric	stomach
26	chr15:75316800-75321800	Weak transcription	Left Ventricle	heart
27	chr15:75316800-75321800	Weak transcription	Ovary	ovary
28	chr15:75316800-75321800	Weak transcription	Right Atrium	heart
29	chr15:75316800-75321800	Weak transcription	Right Ventricle	heart
30	chr15:75316800-75321800	Weak transcription	Small Intestine	intestine
31	chr15:75316800-75321800	Weak transcription	HSMM	muscle
32	chr15:75316800-75321800	Weak transcription	NH-A	brain
33	chr15:75316800-75321800	Weak transcription	NHDF-Ad	bronchial
34	chr15:75316800-75321800	Weak transcription	NHLF	lung
35	chr15:75316800-75322000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:75316800-75322000	Weak transcription	Brain Angular Gyrus	brain
37	chr15:75316800-75322000	Weak transcription	Fetal Brain Male	brain
38	chr15:75316800-75322000	Weak transcription	Psoas Muscle	Psoas
39	chr15:75316800-75322000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:75316800-75322600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:75316800-75322800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:75316800-75338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:75317000-75321800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:75317000-75321800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr15:75317000-75321800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:75317000-75321800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr15:75317000-75322000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:75317200-75321200	Strong transcription	Fetal Stomach	stomach
49	chr15:75317200-75321400	Weak transcription	Primary B cells from cord blood	blood
50	chr15:75317200-75321400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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