Variant report

Variant	rs13379875
Chromosome Location	chr15:73342781-73342782
allele	C/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	GATA3	chr15:73342583-73343273	SH-SY5Y	brain:	n/a	chr15:73343036-73343047
2	MXI1	chr15:73342653-73346307	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72765203..72766825-chr15:73342381..73345092,2	MCF-7	breast:
2	chr15:73074691..73078350-chr15:73341676..73346479,5	MCF-7	breast:

Variant related genes	Relation type
NEO1	TF binding region
ENSG00000159322	Chromatin interaction
ENSG00000260898	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000261423	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1023924	0.85[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs1038137	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10467948	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11072403	0.81[AMR][1000 genomes]
rs12050774	0.94[CHB][hapmap];0.88[CHD][hapmap]
rs12902768	0.81[CHB][hapmap]
rs1479338	0.94[CHB][hapmap]
rs1479339	0.94[CHB][hapmap]
rs1479340	0.81[CHB][hapmap];0.81[GIH][hapmap]
rs1564345	0.81[CHB][hapmap]
rs17762146	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs17762600	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs17829830	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs17829957	0.94[CHB][hapmap]
rs1871385	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs1964543	0.80[EUR][1000 genomes]
rs2127277	0.81[CHB][hapmap]
rs2169951	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2899784	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs3736510	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs4132535	0.80[CHD][hapmap]
rs4132536	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4375637	0.87[CHB][hapmap]
rs4609810	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4776624	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4776625	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4777590	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55836604	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs55916847	0.83[EUR][1000 genomes]
rs55925663	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56269104	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56377702	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62016793	0.83[EUR][1000 genomes]
rs62016795	0.90[EUR][1000 genomes]
rs62016796	0.87[EUR][1000 genomes]
rs62016797	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62016803	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62016805	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62016806	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62016808	0.80[EUR][1000 genomes]
rs62016809	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62016811	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62016813	0.80[EUR][1000 genomes]
rs62016814	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7165610	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7169083	0.81[CHB][hapmap]
rs7172021	0.81[CHB][hapmap];0.81[GIH][hapmap]
rs7172396	0.80[CHB][hapmap]
rs747872	0.81[CHB][hapmap]
rs747873	0.80[CHB][hapmap];0.91[CHD][hapmap]
rs8026121	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8042700	0.81[CHB][hapmap]
rs9920186	0.80[CHD][hapmap]
rs9972347	0.84[AMR][1000 genomes];0.84[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	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13379875	CIITA	trans	parietal	SCAN
rs13379875	THAP10	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73336000-73343200	Weak transcription	Fetal Brain Female	brain
2	chr15:73339200-73343400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:73339400-73343600	Weak transcription	Pancreas	Pancrea
4	chr15:73339600-73343200	Weak transcription	Fetal Brain Male	brain
5	chr15:73341000-73342800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:73341400-73343000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:73341400-73343200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:73341600-73342800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:73341600-73343400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr15:73341600-73343400	Enhancers	Brain Cingulate Gyrus	brain
11	chr15:73341800-73343200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:73341800-73343200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:73341800-73343200	Enhancers	Fetal Lung	lung
14	chr15:73341800-73343400	Enhancers	Brain Hippocampus Middle	brain
15	chr15:73342000-73343200	Weak transcription	Brain Germinal Matrix	brain
16	chr15:73342000-73343600	Weak transcription	Fetal Stomach	stomach
17	chr15:73342200-73343400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:73342400-73343400	Enhancers	Brain Angular Gyrus	brain
19	chr15:73342600-73343200	Weak transcription	Brain Anterior Caudate	brain
20	chr15:73342600-73343200	Enhancers	Fetal Intestine Large	intestine
21	chr15:73342600-73343400	Weak transcription	Brain Substantia Nigra	brain
22	chr15:73342600-73343600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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