Variant report

Variant	rs7314300
Chromosome Location	chr12:56929344-56929345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10735863	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783786	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876891	0.83[MEX][hapmap]
rs10876897	0.85[EUR][1000 genomes]
rs10876899	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171883	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11171884	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171885	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171887	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11614642	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368065	0.81[CHD][hapmap]
rs12814413	0.85[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]
rs1965307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34900037	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34948728	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782235	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4759247	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]
rs6581097	0.96[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581098	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6581099	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131699	0.80[JPT][hapmap]
rs7132918	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7132965	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7136456	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299656	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7299660	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7303549	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7303717	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7305759	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7313637	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313983	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7975238	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7314300	FUT1	Cis_1M	lymphoblastoid	RTeQTL
rs7314300	ESYT1	cis	cerebellum	SCAN
rs7314300	RBMS2	cis	Esophagus Mucosa	GTEx
rs7314300	ITGA5	cis	cerebellum	SCAN
rs7314300	SNORD59A	cis	cerebellum	SCAN
rs7314300	OR6C76	cis	parietal	SCAN
rs7314300	RBMS2	cis	multi-tissue	Pritchard
rs7314300	RBMS2	Cis_1M	lymphoblastoid	RTeQTL
rs7314300	RBMS2	cis	lymphoblastoid	seeQTL
rs7314300	ATF7	cis	parietal	SCAN
rs7314300	AMHR2	cis	cerebellum	SCAN
rs7314300	RBMS2	cis	Whole Blood	GTEx
rs7314300	RBMS2	cis	Lymphoblastoid	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56916800-56930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:56917000-56958000	Weak transcription	Ovary	ovary
3	chr12:56917200-56956200	Weak transcription	Primary T cells from cord blood	blood
4	chr12:56917200-56959200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:56917400-56931400	Weak transcription	Right Ventricle	heart
6	chr12:56918600-56930000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr12:56919400-56929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:56921200-56930800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:56921400-56933400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:56921400-56956200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:56922000-56933000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:56922000-56935400	Weak transcription	Fetal Lung	lung
13	chr12:56922400-56956200	Weak transcription	HSMM	muscle
14	chr12:56922400-56959200	Weak transcription	Fetal Kidney	kidney
15	chr12:56923200-56949200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:56923400-56929600	Weak transcription	Fetal Intestine Small	intestine
17	chr12:56923400-56931200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:56923600-56930800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:56923600-56931200	Weak transcription	Osteobl	bone
20	chr12:56923600-56933000	Weak transcription	NHEK	skin
21	chr12:56923800-56930800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:56923800-56931000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:56923800-56931000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:56923800-56938800	Weak transcription	HMEC	breast
25	chr12:56923800-56959400	Weak transcription	Aorta	Aorta
26	chr12:56924000-56930400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:56924200-56930800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:56924400-56934200	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:56924800-56930000	Weak transcription	Placenta	Placenta
30	chr12:56924800-56930400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:56924800-56931000	Weak transcription	Adipose Nuclei	Adipose
32	chr12:56924800-56933400	Weak transcription	HUVEC	blood vessel
33	chr12:56924800-56959200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:56925000-56929600	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:56925000-56931000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:56925000-56959200	Weak transcription	HSMMtube	muscle
37	chr12:56925200-56930800	Weak transcription	NHLF	lung
38	chr12:56925400-56931000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:56927200-56929600	Weak transcription	Lung	lung
40	chr12:56927600-56930800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:56927600-56934200	Weak transcription	Fetal Stomach	stomach
42	chr12:56927600-56946800	Weak transcription	Left Ventricle	heart
43	chr12:56928200-56931000	Weak transcription	Hela-S3	cervix
44	chr12:56928200-56932400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:56928400-56929800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:56928400-56952400	Weak transcription	Fetal Intestine Large	intestine
47	chr12:56929000-56930000	Weak transcription	A549	lung
48	chr12:56929200-56929800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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