Variant report

Variant	rs2861442
Chromosome Location	chr10:44884959-44884960
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	chr10:44882608..44885734-chr10:44887032..44891125,3	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11239028	0.81[EUR][1000 genomes]
rs17156287	0.96[ASN][1000 genomes]
rs17482472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17540492	0.85[AFR][1000 genomes]
rs17879548	0.96[ASN][1000 genomes]
rs17880358	0.96[ASN][1000 genomes]
rs17880777	0.85[AFR][1000 genomes]
rs17880863	0.96[ASN][1000 genomes]
rs17881575	0.96[ASN][1000 genomes]
rs17883339	0.95[ASN][1000 genomes]
rs17885289	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs197452	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs266088	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs2839679	0.90[AFR][1000 genomes]
rs2839680	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839682	1.00[ASN][1000 genomes]
rs2839683	0.84[AFR][1000 genomes]
rs2839684	0.96[ASN][1000 genomes]
rs2839686	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];0.93[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839687	0.84[AFR][1000 genomes]
rs2839689	0.94[YRI][hapmap]
rs2839690	0.90[LWK][hapmap];0.94[YRI][hapmap]
rs2839692	0.90[LWK][hapmap];0.94[YRI][hapmap]
rs2839695	0.90[LWK][hapmap];0.94[YRI][hapmap]
rs2861441	0.90[AFR][1000 genomes]
rs3780891	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4520554	0.85[AFR][1000 genomes]
rs7082547	0.90[AFR][1000 genomes]
rs7088876	0.84[AFR][1000 genomes]
rs7092453	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs7093481	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72790861	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790862	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs728142	1.00[ASN][1000 genomes]
rs7915848	0.90[LWK][hapmap];0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054649	chr10:44848921-44889713	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv895090	chr10:44874867-44884959	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv895091	chr10:44875040-44888130	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv895092	chr10:44875166-44884959	Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv895093	chr10:44876461-44884959	Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv895094	chr10:44876499-44884959	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv895095	chr10:44876586-44884959	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv895096	chr10:44876586-44886206	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv895097	chr10:44876586-44888130	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv895099	chr10:44878114-44884959	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	nsv895100	chr10:44878835-44884959	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2861442	SYT15	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44882600-44885800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:44882600-44885800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr10:44882600-44885800	Weak transcription	HepG2	liver
4	chr10:44882600-44885800	Weak transcription	Osteobl	bone
5	chr10:44882800-44885800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:44882800-44885800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr10:44883800-44886200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:44884000-44885400	Enhancers	Fetal Heart	heart
9	chr10:44884200-44885000	Enhancers	Adipose Nuclei	Adipose
10	chr10:44884200-44885000	Enhancers	Right Atrium	heart
11	chr10:44884200-44885000	Enhancers	Right Ventricle	heart
12	chr10:44884200-44885000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr10:44884200-44885000	Enhancers	Spleen	Spleen
14	chr10:44884200-44885400	Enhancers	Fetal Muscle Leg	muscle
15	chr10:44884200-44886800	Enhancers	Liver	Liver
16	chr10:44884400-44885000	Enhancers	Left Ventricle	heart
17	chr10:44884600-44885000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:44884600-44885000	Enhancers	Fetal Stomach	stomach
19	chr10:44884600-44885000	Enhancers	Psoas Muscle	Psoas
20	chr10:44884600-44885000	Enhancers	NHDF-Ad	bronchial
21	chr10:44884600-44885200	Enhancers	Fetal Lung	lung
22	chr10:44884600-44885400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr10:44884600-44885400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr10:44884800-44885000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr10:44884800-44885000	Enhancers	Lung	lung
26	chr10:44884800-44885200	Enhancers	Pancreas	Pancrea
27	chr10:44884800-44886400	Enhancers	Fetal Muscle Trunk	muscle

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