Variant report

Variant	rs7068965
Chromosome Location	chr10:99256557-99256558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr10:99256529-99256724	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99205729..99207747-chr10:99256104..99259230,4	MCF-7	breast:
2	chr10:99184102..99187983-chr10:99256299..99259028,4	MCF-7	breast:
3	chr10:99255590..99258774-chr10:99331777..99334688,4	MCF-7	breast:
4	chr10:99255036..99258001-chr10:99391751..99393858,2	K562	blood:
5	chr10:99204416..99207741-chr10:99255231..99259773,5	K562	blood:
6	chr10:99256533..99260506-chr10:99329939..99335950,10	MCF-7	breast:
7	chr10:99230735..99233202-chr10:99255020..99257889,3	MCF-7	breast:
8	chr10:99249819..99251861-chr10:99254679..99256807,3	MCF-7	breast:

No data

Variant related genes	Relation type
UBTD1	TF binding region
ENSG00000171311	Chromatin interaction
ENSG00000171307	Chromatin interaction
ENSG00000171160	Chromatin interaction
ENSG00000224474	Chromatin interaction
ENSG00000171314	Chromatin interaction
ENSG00000165887	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10786349	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap]
rs10882938	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10882941	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs10882942	1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs10882948	0.81[ASN][1000 genomes]
rs11189240	0.93[ASN][1000 genomes]
rs11189245	0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12412017	0.95[ASN][1000 genomes]
rs2007349	0.88[ASN][1000 genomes]
rs2152092	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs2211243	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236575	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3740526	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3750558	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3818909	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[MEX][hapmap]
rs4917773	0.85[ASN][1000 genomes]
rs7093946	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs7096611	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7897727	0.87[CHB][hapmap]
rs7923541	0.81[CHB][hapmap]
rs7923913	0.86[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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7068965	MSX1	trans	lymphoblastoid	seeQTL
rs7068965	MMS19	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99239400-99257400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:99240800-99257400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:99241200-99256800	Weak transcription	Colonic Mucosa	Colon
4	chr10:99241200-99256800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr10:99244200-99257200	Weak transcription	Placenta	Placenta
6	chr10:99250600-99256800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:99250800-99256600	Weak transcription	NHLF	lung
8	chr10:99250800-99256800	Weak transcription	Aorta	Aorta
9	chr10:99250800-99257400	Weak transcription	Ovary	ovary
10	chr10:99251000-99256800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr10:99251200-99256600	Weak transcription	Liver	Liver
12	chr10:99251200-99256800	Weak transcription	HSMMtube	muscle
13	chr10:99252200-99257200	Enhancers	Brain Cingulate Gyrus	brain
14	chr10:99253000-99256600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr10:99253000-99257000	Enhancers	Brain Anterior Caudate	brain
16	chr10:99253000-99257200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr10:99253000-99257200	Enhancers	Right Atrium	heart
18	chr10:99253200-99257200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr10:99253400-99257000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr10:99253400-99257200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:99253400-99257200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr10:99253600-99256600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr10:99253600-99256800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr10:99253600-99257000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr10:99253600-99257200	Enhancers	Fetal Heart	heart
26	chr10:99253800-99256800	Enhancers	Brain Germinal Matrix	brain
27	chr10:99253800-99257200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr10:99253800-99257200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr10:99254000-99256800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr10:99254000-99256800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr10:99254000-99256800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr10:99254200-99256800	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr10:99254200-99256800	Enhancers	HepG2	liver
34	chr10:99254200-99256800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr10:99254200-99257200	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr10:99254400-99256600	Enhancers	Fetal Brain Female	brain
37	chr10:99254400-99256800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr10:99254400-99256800	Enhancers	NHEK	skin
39	chr10:99254400-99257200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr10:99254400-99257400	Enhancers	Fetal Lung	lung
41	chr10:99254600-99256800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:99254600-99257400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:99254800-99256600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr10:99254800-99256800	Enhancers	NH-A	brain
45	chr10:99254800-99257200	Enhancers	Primary B cells from peripheral blood	blood
46	chr10:99254800-99257200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr10:99255000-99256600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:99255000-99256600	Genic enhancers	Fetal Intestine Small	intestine
49	chr10:99255000-99256800	Enhancers	Brain Angular Gyrus	brain
50	chr10:99255000-99256800	Enhancers	Duodenum Mucosa	Duodenum

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