Variant report

Variant	rs2399449
Chromosome Location	chr3:112400174-112400175
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	chr3:112387695..112389279-chr3:112399401..112402386,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11927615	0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12054001	0.84[ASN][1000 genomes]
rs1249910	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1249929	0.88[EUR][1000 genomes]
rs13068244	0.85[EUR][1000 genomes]
rs13088866	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13092258	0.82[EUR][1000 genomes]
rs17457593	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28374264	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3842905	0.81[CHB][hapmap]
rs3843366	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4145150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55894063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56302621	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57211180	0.87[AMR][1000 genomes]
rs58013646	0.86[AMR][1000 genomes]
rs60397548	0.84[ASN][1000 genomes]
rs6768072	0.86[CEU][hapmap];0.87[AMR][1000 genomes]
rs6772102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793555	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7630314	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7633100	0.82[YRI][hapmap]
rs820544	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820545	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9818848	0.81[EUR][1000 genomes]
rs9821100	0.95[CEU][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs9833456	0.82[EUR][1000 genomes]
rs9842816	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9845240	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9864580	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9870933	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs9876497	0.82[EUR][1000 genomes]

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	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2399449	BOC	cis	cerebellum	SCAN
rs2399449	ESAM	trans	parietal	SCAN
rs2399449	LSAMP	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112391400-112407800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:112395800-112400800	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:112396000-112400600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:112396200-112400400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:112396200-112400400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:112396200-112400400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:112396200-112400600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:112396200-112400600	Weak transcription	HUVEC	blood vessel
9	chr3:112396400-112400400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:112396400-112400400	Weak transcription	NH-A	brain
11	chr3:112396400-112400600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:112396400-112400600	Weak transcription	Hela-S3	cervix
13	chr3:112396400-112404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:112396600-112400400	Weak transcription	HMEC	breast
15	chr3:112396600-112400600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:112396600-112400600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:112396600-112400600	Weak transcription	NHEK	skin
18	chr3:112396800-112400200	Weak transcription	Osteobl	bone
19	chr3:112396800-112400400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:112396800-112400600	Weak transcription	HSMMtube	muscle
21	chr3:112397000-112406000	Weak transcription	K562	blood
22	chr3:112397200-112400200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:112397200-112400400	Weak transcription	NHDF-Ad	bronchial
24	chr3:112397400-112400200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:112397400-112400400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:112397400-112400400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:112397400-112401400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:112397400-112405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:112397600-112400400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:112397600-112400400	Weak transcription	NHLF	lung
31	chr3:112397800-112400600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:112398200-112400600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:112398400-112400400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:112398400-112400400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:112398400-112400600	Weak transcription	A549	lung
36	chr3:112400000-112400400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:112400000-112401800	Enhancers	HSMM	muscle

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