Variant report

Variant	rs10876899
Chromosome Location	chr12:56928613-56928614
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10735863	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783786	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876897	0.81[EUR][1000 genomes]
rs10876902	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876903	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171883	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171884	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171885	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171887	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11614642	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12814413	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1965307	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34900037	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34948728	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3782235	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4759247	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6581097	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581098	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581099	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7132918	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7132965	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7136456	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7299115	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7299656	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7299660	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7303549	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7303717	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7305759	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7313637	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7313983	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7314300	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7975238	0.96[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10876899	FUT1	Cis_1M	lymphoblastoid	RTeQTL
rs10876899	RBMS2	cis	Whole Blood	GTEx
rs10876899	RBMS2	cis	Esophagus Mucosa	GTEx
rs10876899	RBMS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 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	chr12:56922200-56928800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:56922400-56956200	Weak transcription	HSMM	muscle
15	chr12:56922400-56959200	Weak transcription	Fetal Kidney	kidney
16	chr12:56923200-56949200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:56923400-56929600	Weak transcription	Fetal Intestine Small	intestine
18	chr12:56923400-56931200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:56923600-56930800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:56923600-56931200	Weak transcription	Osteobl	bone
21	chr12:56923600-56933000	Weak transcription	NHEK	skin
22	chr12:56923800-56930800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:56923800-56931000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:56923800-56931000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:56923800-56938800	Weak transcription	HMEC	breast
26	chr12:56923800-56959400	Weak transcription	Aorta	Aorta
27	chr12:56924000-56930400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:56924200-56930800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:56924400-56934200	Weak transcription	Fetal Muscle Leg	muscle
30	chr12:56924800-56930000	Weak transcription	Placenta	Placenta
31	chr12:56924800-56930400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:56924800-56931000	Weak transcription	Adipose Nuclei	Adipose
33	chr12:56924800-56933400	Weak transcription	HUVEC	blood vessel
34	chr12:56924800-56959200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:56925000-56929600	Weak transcription	Colon Smooth Muscle	Colon
36	chr12:56925000-56931000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:56925000-56959200	Weak transcription	HSMMtube	muscle
38	chr12:56925200-56930800	Weak transcription	NHLF	lung
39	chr12:56925400-56931000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:56927200-56929600	Weak transcription	Lung	lung
41	chr12:56927600-56930800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:56927600-56934200	Weak transcription	Fetal Stomach	stomach
43	chr12:56927600-56946800	Weak transcription	Left Ventricle	heart
44	chr12:56927800-56929000	Enhancers	A549	lung
45	chr12:56928200-56931000	Weak transcription	Hela-S3	cervix
46	chr12:56928200-56932400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:56928400-56929800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:56928400-56952400	Weak transcription	Fetal Intestine Large	intestine
49	chr12:56928600-56929200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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