Variant report

Variant	rs3796439
Chromosome Location	chr4:96050373-96050374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10018945	0.91[MEX][hapmap];0.88[TSI][hapmap]
rs10155123	0.82[CEU][hapmap]
rs10155222	0.82[CEU][hapmap]
rs10212627	0.82[CEU][hapmap]
rs10516958	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs11097456	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11097457	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11097458	0.82[CEU][hapmap]
rs12640643	0.80[EUR][1000 genomes]
rs12644188	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12650281	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1347345	0.91[MEX][hapmap];0.88[TSI][hapmap]
rs1365691	0.85[CEU][hapmap];0.95[GIH][hapmap];0.80[EUR][1000 genomes]
rs1369085	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs1434535	0.80[EUR][1000 genomes]
rs1434536	0.82[CEU][hapmap];0.95[GIH][hapmap];0.80[EUR][1000 genomes]
rs1434538	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1434539	0.82[CEU][hapmap];0.95[GIH][hapmap];0.81[EUR][1000 genomes]
rs1434544	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1434545	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs1540403	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs17344975	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs17348139	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17411860	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs1836261	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1863654	0.80[EUR][1000 genomes]
rs1865379	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1966548	0.96[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1970801	0.96[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2114533	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2162450	0.80[EUR][1000 genomes]
rs2241743	0.92[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs2241744	0.82[CEU][hapmap]
rs2289044	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2865397	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755876	0.82[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3775042	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs3796437	0.81[CEU][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796443	0.82[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3821964	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4583767	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699831	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs58399580	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60472405	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6532527	0.91[MEX][hapmap];0.90[TSI][hapmap]
rs6815593	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs6815969	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7664562	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7681920	0.91[MEX][hapmap];0.88[TSI][hapmap]
rs7682651	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs7694043	0.83[MEX][hapmap]
rs7694131	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7694531	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs989383	0.82[CEU][hapmap];0.80[EUR][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	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
rs3796439	BMPR1B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:96016000-96060600	Weak transcription	Thymus	Thymus
2	chr4:96016600-96054200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr4:96024200-96060600	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:96025000-96054600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:96026400-96057000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:96028200-96051600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:96029600-96051000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:96029600-96051000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:96030400-96054200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:96034200-96079200	Weak transcription	Fetal Kidney	kidney
11	chr4:96034800-96060600	Weak transcription	Ovary	ovary
12	chr4:96035600-96051000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:96040000-96051000	Weak transcription	Aorta	Aorta
14	chr4:96044800-96050800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:96045000-96051000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:96047400-96052400	Weak transcription	Fetal Thymus	thymus
17	chr4:96047400-96060600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr4:96049800-96050400	Enhancers	NH-A	brain
19	chr4:96050000-96050600	Flanking Active TSS	A549	lung
20	chr4:96050000-96050800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:96050200-96050400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:96050200-96050400	Enhancers	Osteobl	bone
23	chr4:96050200-96050800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:96050200-96051000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:96050200-96051000	Enhancers	HUVEC	blood vessel
26	chr4:96050200-96051800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:96050200-96051800	Genic enhancers	Dnd41	blood
28	chr4:96050200-96052200	Enhancers	HSMM	muscle

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