Variant report

Variant	rs2305853
Chromosome Location	chr12:10765779-10765780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:10754715..10757719-chr12:10762132..10766161,5	MCF-7	breast:
2	chr1:202926894..202927819-chr12:10765477..10766262,2	Hela-S3	cervix:
3	chr12:10763668..10768180-chr12:10873034..10877438,4	K562	blood:
4	chr12:10764890..10767963-chr12:10824892..10828037,6	MCF-7	breast:
5	chr12:10757768..10761323-chr12:10763648..10767654,5	MCF-7	breast:
6	chr12:10367004..10369055-chr12:10765454..10767041,2	K562	blood:
7	chr12:10759828..10762348-chr12:10763400..10769792,9	K562	blood:
8	chr12:10765594..10766755-chr17:27046488..27047461,3	Hela-S3	cervix:
9	chr12:10763668..10768484-chr12:10873757..10876876,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000060138	Chromatin interaction
ENSG00000111196	Chromatin interaction
ENSG00000255958	Chromatin interaction
ENSG00000159346	Chromatin interaction
ENSG00000060140	Chromatin interaction
ENSG00000198242	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10083164	0.83[JPT][hapmap]
rs1026442	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10431297	0.82[JPT][hapmap]
rs1054396	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1073305	0.82[JPT][hapmap]
rs10743911	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10772334	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10772340	0.82[JPT][hapmap]
rs10772343	0.81[JPT][hapmap]
rs10772347	0.82[JPT][hapmap]
rs10845180	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10845181	0.88[CEU][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10845183	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845185	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10845192	0.82[JPT][hapmap]
rs10845194	0.81[JPT][hapmap]
rs10845195	0.82[JPT][hapmap]
rs10845197	0.80[JPT][hapmap]
rs10845198	0.82[JPT][hapmap]
rs11053877	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11053880	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11053881	0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs11053882	1.00[JPT][hapmap]
rs12306757	0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs12306815	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs12811247	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1870194	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2011295	0.82[LWK][hapmap]
rs2125091	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2168749	0.84[CEU][hapmap]
rs2219382	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2290718	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2418087	0.82[JPT][hapmap]
rs2418088	0.82[JPT][hapmap]
rs2900513	0.82[JPT][hapmap]
rs3759264	1.00[JPT][hapmap]
rs3759265	0.93[JPT][hapmap]
rs3782674	1.00[JPT][hapmap]
rs4763565	0.89[ASN][1000 genomes]
rs6488316	0.82[JPT][hapmap]
rs7312261	1.00[JPT][hapmap]
rs7313620	0.81[JPT][hapmap]
rs7350557	0.82[JPT][hapmap]
rs7350597	0.82[JPT][hapmap]
rs7968284	0.82[JPT][hapmap]
rs7968819	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971142	0.82[JPT][hapmap]
rs897880	1.00[JPT][hapmap]
rs897882	1.00[JPT][hapmap]
rs9988929	0.96[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2305853	LOC653113	cis	cerebellum	SCAN
rs2305853	TPI1	cis	parietal	SCAN
rs2305853	C1R	cis	parietal	SCAN
rs2305853	GPRC5A	cis	parietal	SCAN
rs2305853	KLRA1	cis	cerebellum	SCAN
rs2305853	NOP2	cis	cerebellum	SCAN
rs2305853	MAGOHB	cis	cerebellum	SCAN
rs2305853	SLC2A14	cis	parietal	SCAN
rs2305853	CLEC4E	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10764600-10765800	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr12:10764600-10765800	Flanking Active TSS	Liver	Liver
3	chr12:10764600-10765800	Flanking Active TSS	Fetal Brain Female	brain
4	chr12:10764600-10766800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:10764600-10766800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr12:10764600-10767000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:10764600-10767200	Active TSS	K562	blood
8	chr12:10764800-10765800	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr12:10764800-10766000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:10764800-10766000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:10764800-10766800	Active TSS	GM12878-XiMat	blood
12	chr12:10764800-10767000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr12:10764800-10767000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr12:10764800-10767000	Active TSS	Fetal Intestine Large	intestine
15	chr12:10764800-10767000	Active TSS	Right Ventricle	heart
16	chr12:10764800-10767200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:10764800-10767200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr12:10764800-10767200	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr12:10764800-10767200	Active TSS	Right Atrium	heart
20	chr12:10765000-10765800	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr12:10765000-10765800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr12:10765000-10765800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr12:10765000-10765800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr12:10765000-10765800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr12:10765000-10765800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr12:10765000-10765800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr12:10765000-10766600	Active TSS	Muscle Satellite Cultured Cells	--
28	chr12:10765000-10766800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr12:10765000-10766800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:10765000-10766800	Active TSS	Left Ventricle	heart
31	chr12:10765000-10766800	Active TSS	Rectal Smooth Muscle	rectum
32	chr12:10765000-10767000	Active TSS	Fetal Muscle Trunk	muscle
33	chr12:10765000-10767000	Active TSS	Fetal Stomach	stomach
34	chr12:10765000-10767000	Active TSS	NHDF-Ad	bronchial
35	chr12:10765000-10767200	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr12:10765000-10767200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:10765000-10767200	Active TSS	Fetal Intestine Small	intestine
38	chr12:10765200-10765800	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr12:10765200-10765800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:10765200-10765800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:10765200-10765800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr12:10765200-10765800	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr12:10765200-10765800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr12:10765200-10765800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr12:10765200-10766000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:10765200-10766000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr12:10765200-10766200	Bivalent/Poised TSS	HepG2	liver
48	chr12:10765200-10766600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:10765200-10766800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:10765200-10766800	Active TSS	HUES6 Cell Line	embryonic stem cell

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