Variant report

Variant	rs10876897
Chromosome Location	chr12:56920402-56920403
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56919517..56922316-chr12:56981865..56983826,2	K562	blood:
2	chr12:56918887..56922105-chr12:57038272..57040603,3	MCF-7	breast:
3	chr12:56916521..56918137-chr12:56919957..56922129,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207031	Chromatin interaction
ENSG00000201579	Chromatin interaction
ENSG00000110955	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10735863	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10783786	0.85[EUR][1000 genomes]
rs10876899	0.81[EUR][1000 genomes]
rs10876902	0.85[EUR][1000 genomes]
rs10876903	0.85[EUR][1000 genomes]
rs11171883	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11171887	0.85[EUR][1000 genomes]
rs11614642	0.85[EUR][1000 genomes]
rs12814413	0.94[ASN][1000 genomes]
rs1965307	0.85[EUR][1000 genomes]
rs34900037	0.85[EUR][1000 genomes]
rs34948728	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3782235	0.91[ASN][1000 genomes]
rs4759247	0.94[ASN][1000 genomes]
rs6581097	0.85[EUR][1000 genomes]
rs6581098	0.84[EUR][1000 genomes]
rs6581099	0.85[EUR][1000 genomes]
rs7132918	0.85[EUR][1000 genomes]
rs7132965	0.85[EUR][1000 genomes]
rs7136456	0.84[EUR][1000 genomes]
rs7299115	0.85[EUR][1000 genomes]
rs7303549	0.85[EUR][1000 genomes]
rs7303717	0.85[EUR][1000 genomes]
rs7305759	0.85[EUR][1000 genomes]
rs7313637	0.85[EUR][1000 genomes]
rs7313983	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7314300	0.85[EUR][1000 genomes]
rs7975238	0.85[EUR][1000 genomes];0.85[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10876897	FUT1	Cis_1M	lymphoblastoid	RTeQTL
rs10876897	RBMS2	Cis_1M	lymphoblastoid	RTeQTL
rs10876897	RBMS2	cis	multi-tissue	Pritchard
rs10876897	RBMS2	cis	Whole Blood	GTEx
rs10876897	RBMS2	cis	Esophagus Mucosa	GTEx
rs10876897	RBMS2	cis	cerebellar cortex	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56916600-56923200	Weak transcription	Small Intestine	intestine
2	chr12:56916800-56930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:56917000-56920800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:56917000-56920800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:56917000-56921600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:56917000-56923000	Weak transcription	Aorta	Aorta
7	chr12:56917000-56958000	Weak transcription	Ovary	ovary
8	chr12:56917200-56920600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:56917200-56920800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:56917200-56920800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:56917200-56920800	Weak transcription	Stomach Mucosa	stomach
12	chr12:56917200-56923000	Weak transcription	Psoas Muscle	Psoas
13	chr12:56917200-56956200	Weak transcription	Primary T cells from cord blood	blood
14	chr12:56917200-56959200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:56917400-56924600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:56917400-56931400	Weak transcription	Right Ventricle	heart
17	chr12:56918000-56920600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:56918000-56920800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:56918000-56921400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:56918200-56920600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:56918600-56920600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:56918600-56930000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr12:56919400-56920800	Weak transcription	Left Ventricle	heart
24	chr12:56919400-56921600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:56919400-56929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:56919600-56923200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:56919600-56924200	Weak transcription	Spleen	Spleen
28	chr12:56919800-56920600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:56919800-56920600	Enhancers	NHDF-Ad	bronchial
30	chr12:56920000-56920600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:56920000-56920800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:56920000-56921000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:56920000-56921000	Weak transcription	Lung	lung
34	chr12:56920000-56921400	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr12:56920200-56920600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr12:56920200-56920600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr12:56920200-56920600	Enhancers	Fetal Heart	heart
38	chr12:56920200-56920600	Weak transcription	Placenta	Placenta
39	chr12:56920200-56920600	Active TSS	Stomach Smooth Muscle	stomach
40	chr12:56920200-56920800	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr12:56920200-56920800	Enhancers	Fetal Intestine Small	intestine
42	chr12:56920200-56920800	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr12:56920200-56920800	Active TSS	Right Atrium	heart
44	chr12:56920200-56920800	Flanking Active TSS	NHEK	skin
45	chr12:56920200-56921000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr12:56920200-56921000	Flanking Active TSS	HMEC	breast
47	chr12:56920200-56921000	Flanking Active TSS	Osteobl	bone
48	chr12:56920200-56921200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr12:56920200-56921200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:56920200-56921200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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