Variant report

Variant	rs17478430
Chromosome Location	chr15:78406959-78406960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78404966..78407239-chr15:78487303..78489850,2	MCF-7	breast:
2	chr15:78405471..78408380-chr15:78587851..78589863,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11629561	1.00[JPT][hapmap]
rs11630776	1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11631100	1.00[JPT][hapmap]
rs11631653	1.00[JPT][hapmap]
rs11638547	1.00[JPT][hapmap]
rs12910386	1.00[JPT][hapmap]
rs12911405	1.00[JPT][hapmap]
rs12915634	1.00[JPT][hapmap]
rs2011323	1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17478430	CSPG4	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78396200-78421800	Weak transcription	Right Ventricle	heart
2	chr15:78396600-78423800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:78397600-78421400	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:78398400-78423200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:78398600-78413200	Weak transcription	Spleen	Spleen
6	chr15:78400000-78412800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:78400000-78422400	Weak transcription	Brain Germinal Matrix	brain
8	chr15:78400200-78414600	Weak transcription	Fetal Brain Female	brain
9	chr15:78401400-78413000	Weak transcription	Fetal Stomach	stomach
10	chr15:78401400-78414400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:78403800-78412200	Weak transcription	Thymus	Thymus
12	chr15:78405600-78412800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:78405600-78413000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:78405600-78421400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:78406000-78407400	Weak transcription	Brain Anterior Caudate	brain
16	chr15:78406000-78412200	Weak transcription	Fetal Intestine Small	intestine
17	chr15:78406000-78414200	Weak transcription	Fetal Intestine Large	intestine
18	chr15:78406000-78421600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:78406000-78423000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:78406200-78412800	Weak transcription	Fetal Thymus	thymus
21	chr15:78406400-78409600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:78406400-78410000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:78406400-78412400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:78406400-78412400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:78406400-78412600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:78406400-78420000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:78406400-78423000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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