Variant report

Variant	rs1530295
Chromosome Location	chr4:77202762-77202763
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	chr4:77202480..77205980-chr4:77226274..77229049,3	MCF-7	breast:
2	chr4:77068994..77070621-chr4:77200458..77203318,2	K562	blood:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction
ENSG00000118804	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1036788	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097320	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441911	0.92[CEU][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441912	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441916	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530296	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1530297	0.87[ASW][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs1530298	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1969148	0.84[ASN][1000 genomes]
rs1969149	0.84[ASN][1000 genomes]
rs2869872	0.86[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4370157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532316	0.92[YRI][hapmap]
rs768981	0.81[AMR][1000 genomes];0.90[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	nsv461559	chr4:77192838-77204500	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594695	chr4:77192838-77204500	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1530295	FAM47E	cis	cerebellum	SCAN
rs1530295	SCARB2	cis	lymphoblastoid	seeQTL
rs1530295	CCNI	cis	lymphoblastoid	seeQTL
rs1530295	NAAA	cis	parietal	SCAN
rs1530295	FAM47E	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77173800-77215800	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:77186400-77204200	Weak transcription	Aorta	Aorta
3	chr4:77186600-77215000	Weak transcription	Brain Anterior Caudate	brain
4	chr4:77192600-77212200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:77194000-77204200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:77194200-77216400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:77199800-77203600	Enhancers	Liver	Liver
8	chr4:77199800-77204200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:77200800-77202800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:77200800-77203000	Enhancers	Stomach Mucosa	stomach
11	chr4:77201400-77203000	Enhancers	Adipose Nuclei	Adipose
12	chr4:77201400-77203000	Enhancers	Duodenum Mucosa	Duodenum
13	chr4:77201400-77203000	Enhancers	HepG2	liver
14	chr4:77201400-77203600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr4:77201400-77204400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:77201400-77205800	Enhancers	Fetal Intestine Large	intestine
17	chr4:77201600-77203000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr4:77201600-77204600	Enhancers	Fetal Heart	heart
19	chr4:77202200-77202800	Weak transcription	Brain Substantia Nigra	brain
20	chr4:77202400-77203600	Weak transcription	Placenta	Placenta
21	chr4:77202400-77203600	Weak transcription	Gastric	stomach
22	chr4:77202400-77204200	Weak transcription	Colonic Mucosa	Colon
23	chr4:77202400-77204200	Weak transcription	Right Atrium	heart
24	chr4:77202400-77204200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:77202400-77205000	Weak transcription	Pancreas	Pancrea
26	chr4:77202400-77206200	Weak transcription	Psoas Muscle	Psoas
27	chr4:77202400-77217000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:77202400-77221000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:77202600-77204200	Weak transcription	Fetal Intestine Small	intestine
30	chr4:77202600-77204200	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links