Variant report

Variant	rs10108907
Chromosome Location	chr8:119454157-119454158
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	chr8:119453959..119456833-chr8:119457362..119459167,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10094604	0.87[ASN][1000 genomes]
rs10096317	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs10101386	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10109048	0.89[ASN][1000 genomes]
rs10282819	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10283133	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10955877	0.95[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap]
rs10955878	0.87[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10955879	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10955883	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs10955884	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs10955885	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[ASN][1000 genomes]
rs10955886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955887	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs11773916	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11773953	0.87[ASN][1000 genomes]
rs11777111	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11782499	0.91[ASN][1000 genomes]
rs11784091	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11784138	0.85[ASN][1000 genomes]
rs11991196	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11994945	0.91[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12155913	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12156430	0.88[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12544750	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12675551	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs12677506	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12678159	0.91[CHB][hapmap]
rs12679343	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12679866	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12679873	0.86[CHB][hapmap]
rs12681581	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs12681600	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs13248112	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13251051	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13251354	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13251719	0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13253470	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13253764	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13255144	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13260753	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13263320	0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs13265657	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs13269591	0.85[CHB][hapmap]
rs4075614	0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[ASN][1000 genomes]
rs4128894	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs4242578	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4242579	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4242580	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs4375037	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4443692	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4492409	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4493938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4548208	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4601348	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4626637	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4629902	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4631494	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4876416	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4876417	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4876833	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4876835	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4876836	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4876837	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs4876838	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs4876839	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs4876840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4876841	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs4876842	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4876845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59298785	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61636365	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62533427	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6469747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6981538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6982369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6983068	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6985503	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7012582	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812733	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7812880	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7813395	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7825963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7826257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7826375	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7826888	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7830347	0.91[ASN][1000 genomes]
rs7830423	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7831361	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7831501	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7835295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7838464	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7846218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297587	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs9642841	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9643128	0.83[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9643129	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9643130	0.87[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9656927	0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv612047	chr8:118939094-119468609	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1032681	chr8:119153316-119609948	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv539737	chr8:119153316-119609948	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831443	chr8:119390590-119590662	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10108907	MED30	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119448000-119456200	Enhancers	HUVEC	blood vessel
2	chr8:119448600-119454200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr8:119449200-119475400	Weak transcription	Gastric	stomach
4	chr8:119449800-119456000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr8:119450000-119454600	Enhancers	NHDF-Ad	bronchial
6	chr8:119450800-119454200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr8:119451600-119456400	Weak transcription	GM12878-XiMat	blood
8	chr8:119452400-119456000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr8:119452400-119456000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr8:119452600-119454200	Enhancers	Hela-S3	cervix
11	chr8:119452600-119454200	Enhancers	NH-A	brain
12	chr8:119452600-119455800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr8:119452800-119454400	Weak transcription	Spleen	Spleen
14	chr8:119452800-119455200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr8:119452800-119456000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr8:119452800-119456000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr8:119452800-119456000	Weak transcription	Aorta	Aorta
18	chr8:119452800-119456200	Weak transcription	Fetal Lung	lung
19	chr8:119452800-119456400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr8:119453000-119456000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr8:119453200-119454200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr8:119453200-119455400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr8:119453200-119455800	Weak transcription	Fetal Heart	heart
24	chr8:119453200-119462400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr8:119453400-119454600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr8:119453400-119455000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr8:119453400-119455800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr8:119453400-119456000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr8:119453400-119456000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr8:119453400-119456000	Weak transcription	NHLF	lung
31	chr8:119453400-119456200	Weak transcription	A549	lung
32	chr8:119454000-119454200	Enhancers	Ovary	ovary
33	chr8:119454000-119454200	Enhancers	Right Atrium	heart
34	chr8:119454000-119454400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr8:119454000-119454800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:119454000-119455800	Weak transcription	Osteobl	bone

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