Variant report

Variant	rs6532530
Chromosome Location	chr4:96007434-96007435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95970827..95973009-chr4:96005064..96008963,3	MCF-7	breast:
2	chr4:96004208..96009283-chr4:96010834..96014104,5	MCF-7	breast:
3	chr4:95966448..95968999-chr4:96005215..96007562,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138696	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10020105	0.85[AMR][1000 genomes]
rs1035810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036352	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1158368	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158792	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1158793	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12506593	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12644367	0.83[ASN][1000 genomes]
rs13134993	0.81[EUR][1000 genomes]
rs1319809	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17022989	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1816461	0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1816463	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897810	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28392869	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28412242	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28419579	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4512000	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6816834	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822629	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs723367	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661539	0.80[EUR][1000 genomes]
rs7671545	0.81[EUR][1000 genomes]
rs967048	0.86[CEU][hapmap]

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	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv492312	chr4:95823124-96128327	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv830011	chr4:95947560-96103934	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv594907	chr4:95975470-96170439	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6532530	BMPR1B	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:96003800-96011600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:96004800-96009200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:96005600-96008400	Enhancers	HMEC	breast
4	chr4:96005600-96008800	Flanking Active TSS	Dnd41	blood
5	chr4:96005600-96009000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:96005600-96009600	Enhancers	NHEK	skin
7	chr4:96006600-96007800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:96006600-96009200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:96006800-96008000	Enhancers	Primary T cells from cord blood	blood
10	chr4:96006800-96008400	Weak transcription	Stomach Mucosa	stomach
11	chr4:96006800-96009200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:96006800-96015400	Weak transcription	HUVEC	blood vessel
13	chr4:96007000-96007800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:96007000-96008200	Active TSS	Fetal Thymus	thymus
15	chr4:96007000-96008200	Flanking Active TSS	A549	lung
16	chr4:96007000-96009400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:96007000-96014000	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:96007200-96009200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:96007200-96009600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:96007400-96008000	Flanking Active TSS	Thymus	Thymus
21	chr4:96007400-96009800	Enhancers	Hela-S3	cervix

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