Variant report

Variant	rs4680372
Chromosome Location	chr3:157209768-157209769
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156877680..156879425-chr3:157209675..157211718,2	MCF-7	breast:
2	chr3:157205290..157208283-chr3:157209694..157212147,2	K562	blood:

Variant related genes	Relation type
ENSG00000163660	Chromatin interaction
ENSG00000197415	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1011060	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs12494965	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12496305	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12634385	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12634412	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12635273	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs1350149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1378801	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16827688	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16827707	0.91[YRI][hapmap]
rs16827716	0.95[YRI][hapmap]
rs16827747	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2165873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2316337	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2316348	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34316188	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4258914	0.86[CHB][hapmap]
rs4679797	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680369	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62278653	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62278654	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62278655	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62280977	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62280978	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62280979	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62280980	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62280981	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6441133	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67228252	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6779693	0.86[CHB][hapmap]
rs73158530	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9682174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv963284	chr3:157209628-157210772	Enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4680372	C3orf55	cis	parietal	SCAN
rs4680372	RAD9A	trans	cerebellum	SCAN
rs4680372	VEPH1	cis	cerebellum	SCAN
rs4680372	C3orf33	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157185600-157211400	Weak transcription	HSMM	muscle
2	chr3:157187600-157210600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:157194000-157212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:157194400-157210200	Weak transcription	NH-A	brain
5	chr3:157194600-157217000	Weak transcription	Pancreas	Pancrea
6	chr3:157194800-157212000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:157198800-157210400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:157199000-157211600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:157206200-157211200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:157206200-157211200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:157206600-157211800	Weak transcription	NHLF	lung
12	chr3:157206800-157211200	Weak transcription	NHDF-Ad	bronchial
13	chr3:157207000-157211400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:157207200-157211400	Weak transcription	Fetal Kidney	kidney
15	chr3:157207400-157211000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:157208600-157210600	Strong transcription	Osteobl	bone
17	chr3:157209000-157211000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:157209000-157211400	Strong transcription	HUVEC	blood vessel
19	chr3:157209400-157209800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:157209400-157210200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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