Variant report

Variant	rs6676293
Chromosome Location	chr1:170528913-170528914
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:170501214..170502810-chr1:170527424..170529028,2	K562	blood:

Variant related genes	Relation type
ENSG00000120370	Chromatin interaction
ENSG00000231407	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10753816	0.80[ASN][1000 genomes]
rs10919422	0.83[EUR][1000 genomes]
rs10919427	0.89[AFR][1000 genomes]
rs10919428	0.86[AFR][1000 genomes]
rs10919432	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11583564	1.00[CHB][hapmap]
rs11801783	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12071298	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12075840	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12097444	0.86[AFR][1000 genomes]
rs12729774	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12731618	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12743310	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12744632	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12755330	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs2901402	0.82[YRI][hapmap];0.92[AFR][1000 genomes]
rs35392130	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59597526	0.94[AFR][1000 genomes]
rs60696673	0.86[AFR][1000 genomes]
rs6663850	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73029152	0.83[AFR][1000 genomes]
rs7515690	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7552922	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs913257	1.00[JPT][hapmap]
rs9919189	0.80[ASN][1000 genomes]

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	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6676293	GORAB	cis	parietal	SCAN
rs6676293	SCYL3	cis	cerebellum	SCAN
rs6676293	DUSP27	cis	parietal	SCAN
rs6676293	RXRG	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170514000-170532000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:170514400-170532000	Weak transcription	Small Intestine	intestine
3	chr1:170517400-170531800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:170519600-170529200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:170519600-170531400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:170521600-170531400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:170521600-170531600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:170521600-170531600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:170521600-170531600	Weak transcription	Left Ventricle	heart
10	chr1:170521600-170531800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:170521600-170532000	Weak transcription	HepG2	liver
12	chr1:170521600-170532600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:170521800-170531800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:170522000-170529200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:170522000-170531400	Weak transcription	HUVEC	blood vessel
16	chr1:170522000-170531600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:170522000-170531600	Weak transcription	Placenta	Placenta
18	chr1:170522000-170531800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:170522000-170531800	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:170522000-170532000	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:170522200-170531600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:170522200-170531600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:170522200-170531800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:170522200-170532000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:170522200-170532000	Weak transcription	K562	blood
26	chr1:170522200-170532200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:170522200-170532400	Weak transcription	Brain Anterior Caudate	brain
28	chr1:170522400-170532000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:170522600-170531400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:170522800-170531400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:170523000-170531600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:170523600-170531800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:170523800-170531800	Weak transcription	Fetal Stomach	stomach
34	chr1:170524000-170531400	Weak transcription	Ovary	ovary
35	chr1:170524000-170531600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:170524200-170529800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:170524800-170529800	Weak transcription	Dnd41	blood
38	chr1:170525200-170530000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:170526600-170530600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:170527200-170531000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:170527200-170531400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:170527600-170530200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:170528200-170532800	Weak transcription	Aorta	Aorta
44	chr1:170528800-170529000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:170528800-170532200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links