Variant report

Variant	rs37535
Chromosome Location	chr5:57617403-57617404
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:57611976..57614758-chr5:57615507..57618157,2	MCF-7	breast:
2	chr5:57615984..57618910-chr5:57754343..57756534,2	MCF-7	breast:
3	chr5:57609295..57611170-chr5:57616223..57618224,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145632	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs151807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs151913	0.96[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs151914	0.91[JPT][hapmap]
rs152011	0.92[CEU][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs152012	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1651127	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs173425	0.83[CHB][hapmap]
rs181764	0.91[JPT][hapmap]
rs184999	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs185425	0.81[ASW][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs190304	0.88[JPT][hapmap]
rs245278	0.82[CHB][hapmap]
rs245481	0.91[JPT][hapmap]
rs245491	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs245494	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap]
rs246113	0.87[GIH][hapmap]
rs2910578	0.84[JPT][hapmap]
rs2910606	0.81[JPT][hapmap]
rs37518	0.81[JPT][hapmap]
rs37537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37538	0.91[EUR][1000 genomes]
rs41385	0.80[JPT][hapmap]
rs42964	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7715909	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3489100	chr5:57545689-57669673	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3489101	chr5:57545689-57669673	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs37535	GAPT	cis	parietal	SCAN
rs37535	SKIV2L2	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57611000-57618200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:57611000-57618400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:57611000-57618400	Weak transcription	HMEC	breast
4	chr5:57611200-57618600	Weak transcription	NHEK	skin
5	chr5:57611400-57617600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:57611800-57618200	Weak transcription	A549	lung
7	chr5:57613200-57618400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:57613400-57618200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:57614600-57618200	Weak transcription	HSMM	muscle
10	chr5:57614800-57617600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:57614800-57617800	Weak transcription	NHDF-Ad	bronchial
12	chr5:57614800-57618000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:57615000-57617600	Weak transcription	HUVEC	blood vessel
14	chr5:57615000-57617800	Weak transcription	Osteobl	bone
15	chr5:57616400-57620200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr5:57616600-57619800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:57616800-57617800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr5:57616800-57617800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:57617000-57617600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:57617200-57617600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:57617200-57617800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr5:57617400-57617800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr5:57617400-57618200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr5:57617400-57618400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:57617400-57618400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:57617400-57619600	Enhancers	HUES6 Cell Line	embryonic stem cell

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