Variant report

Variant	rs10508279
Chromosome Location	chr10:4300734-4300735
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:3826008..3828712-chr10:4299777..4301639,2	MCF-7	breast:
2	chr10:4243895..4246337-chr10:4299306..4301962,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067082	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1000781	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508278	0.85[EUR][1000 genomes]
rs10751964	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10795144	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10795145	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10795146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10904205	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10904206	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10904207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10904208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10904210	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904211	0.92[CHD][hapmap]
rs11252402	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1535445	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535446	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535448	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1570291	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs2025163	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065089	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2146056	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4584476	0.86[JPT][hapmap]
rs4881303	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6601824	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.85[AMR][1000 genomes]
rs6601825	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7081360	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7475965	0.85[EUR][1000 genomes]
rs927411	0.98[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799113	chr10:4259123-4332824	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv1800792	chr10:4259123-4332824	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1820112	chr10:4259123-4332824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv1822419	chr10:4259123-4332824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1839293	chr10:4259123-4332824	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1841782	chr10:4259123-4332824	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1044535	chr10:4271872-4306421	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1053322	chr10:4279301-4306798	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1052378	chr10:4286880-4307024	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1043787	chr10:4286880-4307322	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv1036103	chr10:4286880-4311792	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv2757363	chr10:4286880-4323493	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv2759728	chr10:4286880-4323493	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv1050694	chr10:4290802-4306798	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv3458618	chr10:4293384-4311663	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv3458507	chr10:4293418-4311634	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv3458730	chr10:4293489-4311565	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1037897	chr10:4294071-4311585	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10508279	KLF6	cis	parietal	SCAN
rs10508279	IDI2	cis	parietal	SCAN
rs10508279	ASB13	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4289400-4301400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:4292800-4301800	Weak transcription	Hela-S3	cervix
3	chr10:4296800-4302200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr10:4296800-4308800	Weak transcription	Psoas Muscle	Psoas
5	chr10:4297000-4302000	Weak transcription	Osteobl	bone
6	chr10:4297000-4302200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:4297000-4302200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr10:4297000-4302200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr10:4297600-4302200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:4298200-4305800	Weak transcription	Aorta	Aorta
11	chr10:4298400-4302200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr10:4298400-4302400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr10:4298600-4302400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr10:4298600-4302400	Weak transcription	NHEK	skin
15	chr10:4298800-4300800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr10:4298800-4302600	Weak transcription	HMEC	breast
17	chr10:4300000-4302200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:4300200-4300800	Enhancers	Gastric	stomach
19	chr10:4300200-4300800	Enhancers	Dnd41	blood
20	chr10:4300200-4301000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr10:4300200-4302200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr10:4300400-4301400	Weak transcription	Right Atrium	heart
23	chr10:4300400-4302200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:4300600-4301200	Weak transcription	Ovary	ovary
25	chr10:4300600-4301400	Weak transcription	Spleen	Spleen
26	chr10:4300600-4302000	Weak transcription	NHDF-Ad	bronchial
27	chr10:4300600-4302200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:4300600-4306000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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