Variant report

Variant	rs1008459
Chromosome Location	chr1:175151183-175151184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175150062..175151870-chr1:175152448..175154520,2	MCF-7	breast:
2	chr1:175150391..175152928-chr1:175161401..175163000,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235750	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12136973	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs2205604	0.95[ASN][1000 genomes]
rs2272785	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861158	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs3753559	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3753560	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3766686	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766690	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs3766691	0.85[CEU][hapmap];0.81[CHB][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap]
rs3766695	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522101	chr1:175109517-175151183	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv528874	chr1:175140319-175151183	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1008459	GORAB	cis	parietal	SCAN
rs1008459	FMO1	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175129200-175159600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:175130200-175152600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:175135000-175152600	Weak transcription	Aorta	Aorta
4	chr1:175135000-175158400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:175136000-175151600	Weak transcription	Fetal Stomach	stomach
6	chr1:175136000-175157600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:175141000-175160200	Weak transcription	HUVEC	blood vessel
8	chr1:175141400-175158400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:175143000-175160800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:175143600-175158000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:175145800-175152600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:175146000-175157800	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr1:175146200-175159400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:175146200-175159800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:175146600-175155600	Weak transcription	Ovary	ovary
16	chr1:175146800-175160400	Weak transcription	Fetal Intestine Large	intestine
17	chr1:175147000-175153800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:175147000-175155600	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:175147000-175156200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:175147200-175151400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:175147200-175155600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:175147600-175160400	Weak transcription	Colonic Mucosa	Colon
23	chr1:175147800-175151400	Weak transcription	Liver	Liver
24	chr1:175147800-175151800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:175148000-175151600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:175148000-175151800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:175148000-175153400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:175148200-175151600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:175148200-175157400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:175148200-175157600	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:175148200-175157800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:175148400-175159200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:175148600-175151600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:175148600-175152000	Weak transcription	Gastric	stomach
35	chr1:175148600-175152200	Weak transcription	Fetal Intestine Small	intestine
36	chr1:175148600-175154800	Genic enhancers	Primary B cells from cord blood	blood
37	chr1:175148800-175151800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr1:175148800-175158000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr1:175149200-175151200	Weak transcription	Primary T cells from cord blood	blood
40	chr1:175149200-175151400	Enhancers	Spleen	Spleen
41	chr1:175149400-175151600	Weak transcription	Right Atrium	heart
42	chr1:175149400-175152800	Weak transcription	Esophagus	oesophagus
43	chr1:175149600-175151200	Weak transcription	Adipose Nuclei	Adipose
44	chr1:175149600-175152200	Enhancers	HMEC	breast
45	chr1:175149800-175151200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:175149800-175151400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:175149800-175151400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:175149800-175151800	Weak transcription	Right Ventricle	heart
49	chr1:175149800-175153600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:175149800-175153600	Weak transcription	Small Intestine	intestine

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