Variant report

Variant	rs4759247
Chromosome Location	chr12:56918834-56918835
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56916433..56918956-chr12:56923495..56926214,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10735863	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783786	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876891	0.81[CEU][hapmap];0.96[MEX][hapmap]
rs10876897	0.94[ASN][1000 genomes]
rs10876899	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876902	0.89[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10876903	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11171883	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11171884	0.80[EUR][1000 genomes]
rs11171887	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11614642	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12814413	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965307	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2638285	0.81[LWK][hapmap]
rs2638334	0.81[LWK][hapmap]
rs34900037	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34948728	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3782235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581097	0.84[CEU][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6581098	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6581099	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7131699	0.80[JPT][hapmap]
rs7132918	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7132965	0.89[EUR][1000 genomes]
rs7136456	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7299115	0.89[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7303549	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7303717	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7305759	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7313637	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7313983	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7314300	0.89[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7975238	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4759247	RBMS2	Cis_1M	lymphoblastoid	RTeQTL
rs4759247	RBMS2	cis	Esophagus Mucosa	GTEx
rs4759247	ITGA5	cis	cerebellum	SCAN
rs4759247	RBMS2	cis	multi-tissue	Pritchard
rs4759247	AMHR2	cis	cerebellum	SCAN
rs4759247	OR6C76	cis	parietal	SCAN
rs4759247	FUT1	Cis_1M	lymphoblastoid	RTeQTL
rs4759247	RBMS2	cis	lymphoblastoid	seeQTL
rs4759247	SNORD59A	cis	cerebellum	SCAN
rs4759247	ATF7	cis	parietal	SCAN
rs4759247	RBMS2	cis	Lymphoblastoid	GTEx
rs4759247	RBMS2	cis	Whole Blood	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56914000-56919200	Weak transcription	Spleen	Spleen
2	chr12:56915200-56919000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:56916600-56923200	Weak transcription	Small Intestine	intestine
4	chr12:56916800-56920200	Weak transcription	HepG2	liver
5	chr12:56916800-56930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:56917000-56920200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:56917000-56920200	Weak transcription	Fetal Heart	heart
8	chr12:56917000-56920800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:56917000-56920800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:56917000-56921600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:56917000-56923000	Weak transcription	Aorta	Aorta
12	chr12:56917000-56958000	Weak transcription	Ovary	ovary
13	chr12:56917200-56920200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:56917200-56920200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:56917200-56920200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:56917200-56920400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:56917200-56920600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:56917200-56920800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:56917200-56920800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:56917200-56920800	Weak transcription	Stomach Mucosa	stomach
21	chr12:56917200-56923000	Weak transcription	Psoas Muscle	Psoas
22	chr12:56917200-56956200	Weak transcription	Primary T cells from cord blood	blood
23	chr12:56917200-56959200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:56917400-56920200	Weak transcription	Fetal Thymus	thymus
25	chr12:56917400-56924600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:56917400-56931400	Weak transcription	Right Ventricle	heart
27	chr12:56917600-56919800	Weak transcription	Fetal Muscle Leg	muscle
28	chr12:56917600-56920200	Weak transcription	HSMMtube	muscle
29	chr12:56918000-56919000	Weak transcription	Fetal Stomach	stomach
30	chr12:56918000-56919400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:56918000-56920200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:56918000-56920200	Weak transcription	Fetal Intestine Large	intestine
33	chr12:56918000-56920200	Weak transcription	Fetal Kidney	kidney
34	chr12:56918000-56920400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:56918000-56920600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:56918000-56920800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:56918000-56921400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:56918200-56919000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:56918200-56919000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:56918200-56919200	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:56918200-56919800	Weak transcription	NHDF-Ad	bronchial
42	chr12:56918200-56920200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:56918200-56920200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:56918200-56920200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:56918200-56920200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:56918200-56920200	Weak transcription	Fetal Intestine Small	intestine
47	chr12:56918200-56920200	Enhancers	Placenta	Placenta
48	chr12:56918200-56920200	Weak transcription	Right Atrium	heart
49	chr12:56918200-56920400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:56918200-56920600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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