Variant report

Variant	rs1978107
Chromosome Location	chr12:120101714-120101715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120099358..120101921-chr12:120105818..120108190,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248636	Chromatin interaction
ENSG00000111725	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10849688	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849690	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11064849	0.82[AMR][1000 genomes]
rs11064873	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs175878	0.83[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978108	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs202983	0.80[MEX][hapmap]
rs278102	0.80[TSI][hapmap]
rs278123	0.83[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278126	0.80[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs278143	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278144	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278145	1.00[ASW][hapmap];0.83[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278147	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278148	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278149	0.83[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278151	0.83[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278152	0.83[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278154	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278155	0.83[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930004	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4213	0.83[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490266	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490267	0.93[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304996	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310266	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952841	0.81[AMR][1000 genomes]
rs7960723	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963248	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967558	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972600	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979627	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804667	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052595	chr12:119992580-120132038	Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv541616	chr12:119992580-120132038	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1978107	WSB2	cis	cerebellum	SCAN
rs1978107	COQ5	cis	parietal	SCAN
rs1978107	PRKAB1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120098200-120102600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr12:120098400-120103600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:120098400-120103600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:120098400-120103600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:120098600-120103600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr12:120100400-120103600	Weak transcription	Spleen	Spleen
7	chr12:120100400-120105200	Weak transcription	Psoas Muscle	Psoas
8	chr12:120100600-120102800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr12:120100600-120104000	Weak transcription	HUVEC	blood vessel
10	chr12:120101000-120103000	Enhancers	K562	blood
11	chr12:120101400-120102400	Weak transcription	HepG2	liver

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