Variant report

Variant	rs285754
Chromosome Location	chr15:93176493-93176494
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	chr15:93143236..93145258-chr15:93175927..93177616,2	MCF-7	breast:
2	chr15:93165242..93167435-chr15:93175583..93177925,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12443091	0.89[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs12593636	1.00[ASN][1000 genomes]
rs12908852	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1496712	0.89[EUR][1000 genomes]
rs1496726	0.89[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs16947098	1.00[ASN][1000 genomes]
rs16947102	1.00[ASN][1000 genomes]
rs16974307	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs184048	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2254142	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453901	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs285755	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285757	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285758	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285766	0.90[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs285772	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366789	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373481	0.84[CEU][hapmap];0.84[MEX][hapmap];0.80[EUR][1000 genomes]
rs406032	0.85[EUR][1000 genomes]
rs413450	0.87[EUR][1000 genomes]
rs426221	1.00[ASN][1000 genomes]
rs434826	0.82[EUR][1000 genomes]
rs503112	0.87[EUR][1000 genomes]
rs6496969	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs7178546	0.90[EUR][1000 genomes]
rs72758232	1.00[ASN][1000 genomes]
rs72758234	1.00[ASN][1000 genomes]
rs72758301	1.00[ASN][1000 genomes]
rs73454725	1.00[ASN][1000 genomes]
rs73454730	1.00[ASN][1000 genomes]
rs893379	0.89[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	esv1808537	chr15:93146057-93191935	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv974717	chr15:93170490-93180185	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs285754	PRC1	cis	parietal	SCAN
rs285754	RGMA	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93151600-93178000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:93161400-93178000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:93163600-93180600	Weak transcription	Small Intestine	intestine
4	chr15:93167000-93177400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:93167800-93178200	Weak transcription	Colonic Mucosa	Colon
6	chr15:93167800-93179800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:93168200-93178000	Weak transcription	Fetal Brain Male	brain
8	chr15:93168200-93178000	Weak transcription	Lung	lung
9	chr15:93168200-93179800	Weak transcription	Spleen	Spleen
10	chr15:93168200-93180200	Weak transcription	Psoas Muscle	Psoas
11	chr15:93168400-93179200	Weak transcription	Adipose Nuclei	Adipose
12	chr15:93168800-93177400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:93168800-93177600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:93169000-93180400	Weak transcription	Fetal Kidney	kidney
15	chr15:93169200-93177800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:93169200-93178000	Weak transcription	Brain Anterior Caudate	brain
17	chr15:93169200-93178400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:93169200-93179200	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:93169200-93180200	Weak transcription	A549	lung
20	chr15:93170000-93177000	Weak transcription	HSMMtube	muscle
21	chr15:93170000-93180400	Weak transcription	HSMM	muscle
22	chr15:93171000-93178000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:93171000-93197400	Weak transcription	Primary T cells from cord blood	blood
24	chr15:93171400-93180200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:93172800-93177400	Weak transcription	Brain Angular Gyrus	brain
26	chr15:93173000-93177600	Weak transcription	Brain Substantia Nigra	brain
27	chr15:93173200-93177600	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:93173600-93176800	Weak transcription	Gastric	stomach
29	chr15:93173600-93177400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:93173600-93177600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:93173600-93177600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:93173600-93177800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:93173600-93178000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:93173600-93178000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:93173600-93179600	Weak transcription	Ovary	ovary
36	chr15:93173600-93179800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:93173600-93180200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:93173800-93176800	Weak transcription	Left Ventricle	heart
39	chr15:93173800-93177000	Weak transcription	Fetal Muscle Leg	muscle
40	chr15:93173800-93177000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr15:93173800-93177200	Weak transcription	Fetal Stomach	stomach
42	chr15:93173800-93177400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr15:93173800-93177600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:93173800-93177600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:93173800-93178200	Weak transcription	Fetal Lung	lung
46	chr15:93173800-93178400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:93173800-93178600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr15:93173800-93179600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:93173800-93179800	Weak transcription	Esophagus	oesophagus
50	chr15:93173800-93179800	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links