Variant report

Variant	rs3950310
Chromosome Location	chr10:49502581-49502582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:49502225..49505206-chr10:49511176..49513041,2	MCF-7	breast:
2	chr10:49497874..49500351-chr10:49502359..49504964,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10218874	0.85[ASN][1000 genomes]
rs10437448	0.92[ASN][1000 genomes]
rs10508901	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10508903	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1051507	0.81[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap]
rs1051509	0.92[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap]
rs10745265	0.80[CHB][hapmap]
rs10745266	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10745269	0.91[ASN][1000 genomes]
rs10745270	0.86[ASN][1000 genomes]
rs10776595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10776596	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10776598	0.87[ASN][1000 genomes]
rs10857560	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10857561	0.87[CHD][hapmap];0.95[JPT][hapmap]
rs10857566	0.92[CEU][hapmap]
rs11101290	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11101298	0.81[ASN][1000 genomes]
rs11101306	0.86[ASN][1000 genomes]
rs11101318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs11101320	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap]
rs12411830	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1345103	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1919708	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1919712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1919713	0.85[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1997365	0.80[CHB][hapmap];0.80[MEX][hapmap]
rs2017750	0.84[CHB][hapmap];0.95[CHD][hapmap]
rs2263102	0.87[ASN][1000 genomes]
rs2289805	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2377351	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs2440861	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2463959	0.95[JPT][hapmap]
rs2463960	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs2590381	0.87[ASN][1000 genomes]
rs2698761	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs2698766	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2698767	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3827680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs3827681	0.81[CEU][hapmap]
rs4838590	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61840543	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537559	0.80[CHB][hapmap]
rs6537560	0.90[ASN][1000 genomes]
rs6537561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7072515	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7075976	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs7076214	0.85[ASN][1000 genomes]
rs7086070	0.91[ASN][1000 genomes]
rs7086275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap]
rs7101060	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs734371	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs7898026	0.80[CHB][hapmap]
rs7912697	0.83[ASN][1000 genomes]
rs8428	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap]
rs867631	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs883604	0.90[ASN][1000 genomes]
rs9284	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9888128	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550812	chr10:49484698-49524715	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3950310	SGMS1	cis	parietal	SCAN
rs3950310	MAPK8	cis	normal skin	skin_eQTL
rs3950310	MAPK8	cis	Thyroid	GTEx
rs3950310	MAPK8	cis	Esophagus Muscularis	GTEx
rs3950310	MAPK8	cis	cerebellum	SCAN
rs3950310	MAPK8	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49493600-49504200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:49496400-49514200	Weak transcription	Right Atrium	heart
3	chr10:49499800-49503400	Weak transcription	HepG2	liver
4	chr10:49502200-49503400	Enhancers	Placenta	Placenta

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