Variant report

Variant	rs4238339
Chromosome Location	chr15:59785459-59785460
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59466810..59467651-chr15:59784616..59785747,3	MCF-7	breast:
2	chr15:59249330..59250119-chr15:59784856..59785723,2	K562	blood:
3	chr15:59453294..59454240-chr15:59784784..59785726,7	MCF-7	breast:
4	chr15:59272370..59273203-chr15:59785181..59785695,2	K562	blood:
5	chr15:58505987..58508184-chr15:59784928..59787328,2	K562	blood:
6	chr15:59453317..59454057-chr15:59785026..59785536,2	K562	blood:
7	chr15:59785251..59785790-chr15:59793517..59794379,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10450987	0.82[EUR][1000 genomes]
rs12913655	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4291860	1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4296198	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4624109	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774332	0.82[EUR][1000 genomes]
rs4774336	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs7172008	0.82[EUR][1000 genomes]
rs7182428	0.81[EUR][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4238339	CCPG1	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59782400-59785600	Enhancers	Fetal Heart	heart
2	chr15:59783800-59785600	Enhancers	Brain Angular Gyrus	brain
3	chr15:59784000-59788600	Weak transcription	Left Ventricle	heart
4	chr15:59784200-59785600	Enhancers	Primary B cells from cord blood	blood
5	chr15:59784400-59785600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr15:59784400-59785600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:59784400-59785600	Enhancers	A549	lung
8	chr15:59784400-59785600	Enhancers	GM12878-XiMat	blood
9	chr15:59784400-59785600	Enhancers	HepG2	liver
10	chr15:59784600-59785600	Enhancers	H9 Cell Line	embryonic stem cell
11	chr15:59784600-59785600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:59784600-59785600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr15:59784600-59785600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr15:59784600-59785600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:59785000-59785600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr15:59785000-59785600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:59785000-59785600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:59785000-59785600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr15:59785000-59785600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr15:59785000-59785600	Enhancers	Primary B cells from peripheral blood	blood
21	chr15:59785000-59785600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr15:59785000-59785600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr15:59785000-59785600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:59785000-59785600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:59785000-59785600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:59785000-59785600	Enhancers	Adipose Nuclei	Adipose
27	chr15:59785000-59785600	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr15:59785000-59785600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr15:59785000-59785600	Enhancers	Duodenum Mucosa	Duodenum
30	chr15:59785000-59785600	Enhancers	Fetal Intestine Small	intestine
31	chr15:59785000-59785600	Enhancers	Fetal Muscle Leg	muscle
32	chr15:59785000-59785600	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr15:59785000-59785600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr15:59785000-59785600	Enhancers	Right Ventricle	heart
35	chr15:59785000-59785600	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr15:59785200-59785600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr15:59785200-59785600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:59785200-59785600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr15:59785200-59785600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr15:59785200-59785600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr15:59785200-59785600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr15:59785200-59785600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:59785200-59785600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:59785200-59785600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:59785200-59785600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr15:59785200-59785600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr15:59785200-59785600	Bivalent Enhancer	Dnd41	blood
48	chr15:59785200-59785800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:59785400-59785600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:59785400-59785600	Enhancers	Liver	Liver

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