Variant report

Variant	rs12520230
Chromosome Location	chr5:107141575-107141576
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:107141560-107141710	BE2_C	brain:	n/a	chr5:107141651-107141664
2	ZNF263	chr5:107141483-107142404	HEK293-T-REx	kidney:	n/a	chr5:107142099-107142108 chr5:107142085-107142106

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:107125029..107126613-chr5:107139861..107141985,2	MCF-7	breast:

Variant related genes	Relation type
RN7SKP122	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10515380	0.82[ASN][1000 genomes]
rs12186563	0.82[ASN][1000 genomes]
rs12187616	0.82[ASN][1000 genomes]
rs12189428	0.90[MEX][hapmap]
rs12513976	0.82[ASN][1000 genomes]
rs12519254	0.90[MEX][hapmap]
rs12522548	0.90[MEX][hapmap]
rs12522552	0.83[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap]
rs17160706	0.80[MEX][hapmap]
rs17369104	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17435188	0.82[ASN][1000 genomes]
rs3842914	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3842915	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843491	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843492	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355954	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62355956	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6864994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736608	0.96[EUR][1000 genomes];1.00[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	nsv830440	chr5:107074116-107278905	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv969928	chr5:107132237-107143800	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1022155	chr5:107138981-107149604	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12520230	CAMK4	cis	cerebellum	SCAN
rs12520230	SLC25A46	cis	cerebellum	SCAN
rs12520230	FBXL17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107135400-107143000	Weak transcription	Right Atrium	heart
2	chr5:107138400-107144800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:107139800-107142000	Weak transcription	NHDF-Ad	bronchial
4	chr5:107140200-107144200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:107140200-107144400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr5:107140400-107144000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr5:107140400-107144000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:107140400-107144200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:107140400-107148800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:107140600-107142800	Enhancers	H9 Cell Line	embryonic stem cell
11	chr5:107140600-107144000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr5:107140800-107141600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr5:107140800-107142400	Enhancers	Brain Germinal Matrix	brain
14	chr5:107140800-107142800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:107140800-107144400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:107140800-107145000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr5:107140800-107146600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:107141000-107142000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:107141000-107142800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:107141000-107143800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:107141200-107142200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:107141200-107144400	Weak transcription	Dnd41	blood
23	chr5:107141400-107141600	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr5:107141400-107144200	Weak transcription	Fetal Intestine Large	intestine
25	chr5:107141400-107146000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:107141400-107146600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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