Variant report

Variant	rs6481515
Chromosome Location	chr10:28524497-28524498
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	chr10:28518323..28520452-chr10:28523797..28525301,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10763647	0.81[JPT][hapmap]
rs10763653	0.81[CEU][hapmap]
rs10763654	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10763655	0.95[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10826425	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs10826426	0.81[CEU][hapmap]
rs10826428	0.81[CEU][hapmap]
rs10826433	0.87[ASN][1000 genomes]
rs10826435	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs10826436	0.86[ASN][1000 genomes]
rs10826439	0.80[CEU][hapmap]
rs10826449	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs11006917	0.81[JPT][hapmap]
rs11006931	0.81[CEU][hapmap]
rs11006940	0.81[CEU][hapmap]
rs11006946	0.88[ASN][1000 genomes]
rs11006950	0.87[JPT][hapmap]
rs11006956	0.88[ASN][1000 genomes]
rs11006957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11006959	0.83[ASN][1000 genomes]
rs11006962	0.83[ASN][1000 genomes]
rs11006965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11006970	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1148175	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12251587	0.84[CHD][hapmap]
rs12256403	0.82[CHB][hapmap]
rs12358399	0.80[CEU][hapmap]
rs1418757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17758855	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1840877	0.81[CEU][hapmap]
rs1870097	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.88[ASN][1000 genomes]
rs1870098	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs1937807	0.85[CHD][hapmap]
rs1937808	0.85[CHD][hapmap]
rs1937809	0.86[CHD][hapmap]
rs1953322	0.86[ASN][1000 genomes]
rs1953324	0.82[ASN][1000 genomes]
rs2085471	0.88[ASN][1000 genomes]
rs2100615	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2100616	0.88[ASN][1000 genomes]
rs2124955	0.86[CHB][hapmap]
rs2290701	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607540	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2985535	0.86[CHD][hapmap]
rs2997210	0.86[CHD][hapmap]
rs3847388	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs4568902	0.84[CHD][hapmap]
rs61845911	0.88[ASN][1000 genomes]
rs6481513	0.81[CEU][hapmap]
rs6481514	0.81[CEU][hapmap]
rs7072480	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7072854	0.81[CEU][hapmap]
rs7081371	0.81[CEU][hapmap]
rs7084878	0.81[CEU][hapmap]
rs7088465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7088552	0.83[CHD][hapmap]
rs7096944	0.83[CHD][hapmap]
rs7893304	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7893685	0.81[CEU][hapmap]
rs7905490	0.82[CHB][hapmap]
rs7913970	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7922685	0.84[CHD][hapmap]
rs9664773	0.81[CEU][hapmap]
rs9919516	0.81[ASN][1000 genomes]

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	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv831817	chr10:28369836-28539930	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6481515	MPP7	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28467600-28525600	Weak transcription	Aorta	Aorta
2	chr10:28487600-28529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:28498200-28531200	Weak transcription	Primary B cells from cord blood	blood
4	chr10:28498200-28537000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr10:28502000-28531600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr10:28502400-28525000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr10:28507200-28528600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr10:28507400-28525400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr10:28507400-28530600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr10:28507600-28531000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr10:28510800-28530400	Weak transcription	HSMMtube	muscle
12	chr10:28511000-28528800	Weak transcription	Fetal Heart	heart
13	chr10:28515600-28528000	Weak transcription	Gastric	stomach
14	chr10:28516600-28527400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr10:28516800-28530400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr10:28518400-28531000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr10:28519000-28552000	Weak transcription	Fetal Stomach	stomach
18	chr10:28519800-28528800	Weak transcription	Fetal Intestine Large	intestine
19	chr10:28520400-28525600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr10:28521200-28527600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr10:28521200-28538600	Weak transcription	Left Ventricle	heart
22	chr10:28521800-28529800	Weak transcription	Fetal Intestine Small	intestine
23	chr10:28521800-28544400	Weak transcription	Pancreas	Pancrea
24	chr10:28522000-28526800	Strong transcription	Primary T cells from cord blood	blood
25	chr10:28522000-28527400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr10:28522000-28531400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr10:28522200-28525000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr10:28522200-28527200	Weak transcription	Ovary	ovary
29	chr10:28522400-28537000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr10:28523000-28526200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr10:28523000-28527400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr10:28523200-28524800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr10:28523200-28527400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr10:28523200-28527600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr10:28523400-28530400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr10:28523600-28531400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr10:28523800-28529000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr10:28524000-28527600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr10:28524000-28537000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr10:28524200-28528600	Weak transcription	HepG2	liver
41	chr10:28524200-28537000	Weak transcription	Esophagus	oesophagus
42	chr10:28524400-28530600	Weak transcription	Duodenum Mucosa	Duodenum

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