Variant report

Variant	rs10753229
Chromosome Location	chr1:180920226-180920227
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180920141..180924832-chr1:180927695..180934337,6	MCF-7	breast:
2	chr1:180913861..180917662-chr1:180919365..180922791,5	K562	blood:
3	chr1:180918890..180922237-chr1:180924310..180927954,4	K562	blood:
4	chr1:180900719..180903154-chr1:180917426..180920329,2	MCF-7	breast:
5	chr1:180919620..180921872-chr1:180924310..180926710,2	K562	blood:

Variant related genes	Relation type
ENSG00000251520	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10797664	0.81[MKK][hapmap]
rs11807408	1.00[YRI][hapmap]
rs2068800	0.92[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs4651080	0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs58047756	0.98[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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv872579	chr1:180881148-180931508	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2754938	chr1:180919343-180934343	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10753229	CACNA1E	cis	parietal	SCAN
rs10753229	STX6	cis	cerebellum	SCAN
rs10753229	MR1	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180896800-180921800	Weak transcription	Pancreas	Pancrea
2	chr1:180899000-180922600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:180900000-180922800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:180904800-180922400	Weak transcription	Colonic Mucosa	Colon
5	chr1:180905400-180922400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:180905400-180940600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:180907800-180922400	Weak transcription	NHDF-Ad	bronchial
8	chr1:180908600-180921800	Weak transcription	Right Atrium	heart
9	chr1:180911600-180921600	Weak transcription	Fetal Heart	heart
10	chr1:180911600-180928400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:180911800-180927600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:180912400-180922400	Weak transcription	Stomach Mucosa	stomach
13	chr1:180913200-180921400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:180913400-180921000	Strong transcription	Fetal Intestine Small	intestine
15	chr1:180914800-180922600	Weak transcription	Ovary	ovary
16	chr1:180915400-180922800	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:180915600-180922400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:180916000-180922000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:180916200-180922600	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:180916400-180920800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:180916400-180922400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:180916400-180922600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:180916400-180922600	Weak transcription	HSMM	muscle
24	chr1:180916600-180921800	Weak transcription	HepG2	liver
25	chr1:180916800-180921400	Strong transcription	Fetal Intestine Large	intestine
26	chr1:180916800-180922000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:180916800-180922200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:180916800-180922600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr1:180916800-180922600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:180917000-180920800	Genic enhancers	Dnd41	blood
31	chr1:180917000-180921000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:180917000-180922400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:180917200-180920600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:180917200-180922800	Enhancers	Placenta	Placenta
35	chr1:180917400-180922800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:180917600-180922600	Weak transcription	Brain Germinal Matrix	brain
37	chr1:180917800-180922400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr1:180917800-180922400	Weak transcription	NHEK	skin
39	chr1:180918000-180921200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:180918000-180930000	Weak transcription	HSMMtube	muscle
41	chr1:180918200-180921000	Genic enhancers	Fetal Thymus	thymus
42	chr1:180918200-180922600	Weak transcription	Primary B cells from cord blood	blood
43	chr1:180918200-180922800	Weak transcription	Psoas Muscle	Psoas
44	chr1:180918400-180921200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:180918400-180921400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:180918400-180922400	Weak transcription	HMEC	breast
47	chr1:180918400-180929000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:180918400-180929800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:180918400-180930000	Weak transcription	Hela-S3	cervix
50	chr1:180918600-180920400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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