Variant report

Variant	rs2145048
Chromosome Location	chr6:36557580-36557581
allele	A/C
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	POLR2A	chr6:36557241-36557787	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36513370..36515088-chr6:36555840..36557941,2	MCF-7	breast:
2	chr6:36512934..36515344-chr6:36555459..36558078,2	K562	blood:
3	chr6:36477544..36480238-chr6:36555943..36558724,2	MCF-7	breast:
4	chr6:36537495..36539937-chr6:36557300..36560014,2	K562	blood:

Variant related genes	Relation type
SRSF3	TF binding region
ENSG00000112079	Chromatin interaction
ENSG00000264878	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10214849	0.85[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10223366	0.83[EUR][1000 genomes]
rs1076931	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10807169	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947613	0.87[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947614	0.95[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10947615	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11756557	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11756969	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12153820	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12202732	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208086	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12211825	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1406945	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1812018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1812019	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1812020	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001101	0.86[EUR][1000 genomes]
rs4713987	0.83[EUR][1000 genomes]
rs56144242	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60627328	0.83[EUR][1000 genomes]
rs61211228	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs671516	0.81[EUR][1000 genomes]
rs6913530	0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6937430	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72852338	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72852340	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73410251	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7344	0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7738559	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7738561	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7741888	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7743396	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7747264	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755461	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7759778	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7759933	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7760766	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7767296	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9296193	0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9349001	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357217	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9357218	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9357219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366907	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9366908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366909	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9366911	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9368938	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9368939	0.85[EUR][1000 genomes]
rs9368940	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368942	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs9368943	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380577	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380578	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9380580	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380582	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394359	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394360	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394361	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394362	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9394363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394365	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2145048	MEGF9	trans	cerebellum	SCAN
rs2145048	IP6K3	cis	parietal	SCAN
rs2145048	GLO1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36551600-36558000	Weak transcription	NHDF-Ad	bronchial
2	chr6:36551600-36559600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:36551600-36560000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:36551600-36560600	Weak transcription	Fetal Intestine Small	intestine
5	chr6:36553400-36558000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:36553400-36558000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:36553400-36558000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:36553400-36558000	Weak transcription	HSMMtube	muscle
9	chr6:36553400-36558000	Weak transcription	NH-A	brain
10	chr6:36553400-36561000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:36553800-36558000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:36553800-36558000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:36553800-36558000	Weak transcription	HSMM	muscle
14	chr6:36553800-36558000	Weak transcription	Osteobl	bone
15	chr6:36553800-36561000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:36554600-36561200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:36556200-36560000	Weak transcription	K562	blood
18	chr6:36556400-36558000	Weak transcription	NHEK	skin
19	chr6:36557400-36559400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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