Variant report

Variant	rs4130161
Chromosome Location	chr12:105356797-105356798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105350549..105352894-chr12:105354821..105356979,2	K562	blood:
2	chr12:105355342..105357518-chr12:105358674..105361105,2	K562	blood:
3	chr12:105302265..105304511-chr12:105355863..105357764,2	K562	blood:
4	chr12:105354302..105359267-chr12:105378860..105381853,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136052	Chromatin interaction
ENSG00000151131	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10507183	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs10507185	0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10778354	0.87[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10778356	0.91[ASN][1000 genomes]
rs10861278	0.83[ASN][1000 genomes]
rs10861280	0.81[ASN][1000 genomes]
rs10861282	0.87[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10861291	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10861293	0.89[ASN][1000 genomes]
rs10861295	0.91[ASN][1000 genomes]
rs10861297	0.98[ASN][1000 genomes]
rs11112208	0.82[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11112221	0.84[ASN][1000 genomes]
rs11112234	0.86[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs11112268	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112269	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12230563	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12230637	0.94[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs17829927	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2047126	0.82[ASN][1000 genomes]
rs2245695	0.92[ASN][1000 genomes]
rs2249941	0.90[ASN][1000 genomes]
rs2252843	0.90[ASN][1000 genomes]
rs2264883	0.92[ASN][1000 genomes]
rs2264893	0.91[ASN][1000 genomes]
rs2453163	0.84[ASN][1000 genomes]
rs2453164	0.84[ASN][1000 genomes]
rs2453169	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs2468094	0.80[ASN][1000 genomes]
rs2468096	0.83[ASN][1000 genomes]
rs2468098	0.83[ASN][1000 genomes]
rs2468103	0.84[ASN][1000 genomes]
rs2468107	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2468108	0.84[ASN][1000 genomes]
rs2468336	0.91[ASN][1000 genomes]
rs2468338	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2468339	0.82[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2468341	0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2468342	0.80[ASN][1000 genomes]
rs2468343	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs2468345	0.80[ASN][1000 genomes]
rs2468397	0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2642119	0.84[ASN][1000 genomes]
rs2642120	0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2730294	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs4257060	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4537841	0.97[ASN][1000 genomes]
rs4630370	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4644704	0.87[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs73383489	0.82[AFR][1000 genomes]
rs7959777	0.87[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs7961766	0.89[ASN][1000 genomes]
rs7971260	0.84[ASN][1000 genomes]
rs7971392	0.86[ASN][1000 genomes]
rs9705471	0.89[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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4130161	ASCL1	cis	parietal	SCAN
rs4130161	SLC5A8	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105353200-105357400	Weak transcription	Fetal Brain Male	brain
2	chr12:105353600-105357000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:105353800-105358000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:105353800-105358800	Weak transcription	GM12878-XiMat	blood
5	chr12:105356200-105357600	Weak transcription	Fetal Brain Female	brain
6	chr12:105356600-105356800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:105356600-105359400	Enhancers	Cortex derived primary cultured neurospheres	brain

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