Variant report

Variant	rs12504291
Chromosome Location	chr4:57309663-57309664
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57309121..57311170-chr4:57312040..57313868,2	MCF-7	breast:
2	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
3	chr4:57253395..57255895-chr4:57308484..57311202,2	MCF-7	breast:
4	chr4:57306221..57310097-chr4:57330857..57334001,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269921	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000270109	Chromatin interaction
ENSG00000174780	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10015221	0.87[CEU][hapmap]
rs10434444	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs10434445	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1060472	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11133442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11610	0.80[JPT][hapmap]
rs12498340	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs12501334	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12501502	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12503412	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12508008	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12510712	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12511770	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12513091	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13147900	0.95[JPT][hapmap]
rs1356787	0.80[CEU][hapmap];0.80[JPT][hapmap]
rs1401904	0.95[JPT][hapmap]
rs1401906	0.94[JPT][hapmap]
rs14211	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1474179	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1520026	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1520030	1.00[CEU][hapmap]
rs17051687	0.80[CEU][hapmap]
rs17086696	0.89[JPT][hapmap]
rs17086794	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17086832	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17086853	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1967559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1983378	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs2030366	0.81[AMR][1000 genomes]
rs2049087	0.80[CEU][hapmap]
rs2271923	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs28866881	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3796541	0.81[AMR][1000 genomes]
rs4340842	0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4346704	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4493603	1.00[CEU][hapmap]
rs4618376	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4864579	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs4864583	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4865092	0.89[JPT][hapmap];0.82[AMR][1000 genomes]
rs4865103	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5010012	0.91[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56392224	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58151706	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6554345	0.95[JPT][hapmap]
rs6554358	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6584	0.80[CEU][hapmap];0.80[JPT][hapmap]
rs66810706	0.81[AMR][1000 genomes]
rs66858948	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6816268	0.81[CEU][hapmap]
rs6819534	0.80[CEU][hapmap]
rs6820314	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6821301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6829250	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6830518	0.80[CEU][hapmap];0.80[JPT][hapmap]
rs6832797	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6834696	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6834736	0.95[JPT][hapmap]
rs6848187	0.80[JPT][hapmap]
rs6849183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6855041	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7664841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8340	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs9996593	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12504291	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
2	chr4:57303800-57326000	Weak transcription	Gastric	stomach
3	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
4	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
5	chr4:57304000-57312000	Weak transcription	Left Ventricle	heart
6	chr4:57304000-57315800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
8	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
9	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
10	chr4:57304200-57314600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:57304200-57314800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:57304200-57317400	Weak transcription	Thymus	Thymus
13	chr4:57304200-57318800	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:57304200-57319200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:57304400-57310400	Weak transcription	NHLF	lung
17	chr4:57304400-57312600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:57304400-57314000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:57304400-57314000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:57304400-57314600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:57304400-57314600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:57304400-57314600	Weak transcription	Fetal Brain Female	brain
23	chr4:57304400-57314600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr4:57304400-57314800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:57304400-57314800	Weak transcription	Adipose Nuclei	Adipose
26	chr4:57304400-57314800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:57304400-57315200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:57304400-57315600	Weak transcription	Fetal Stomach	stomach
29	chr4:57304400-57317200	Weak transcription	Ovary	ovary
30	chr4:57304400-57317800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr4:57304400-57318400	Weak transcription	Psoas Muscle	Psoas
32	chr4:57304400-57318600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:57304400-57319800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:57304400-57320200	Weak transcription	Fetal Heart	heart
35	chr4:57304400-57320200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr4:57304400-57321200	Weak transcription	HSMMtube	muscle
37	chr4:57304400-57330800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:57304400-57330800	Weak transcription	Brain Substantia Nigra	brain
39	chr4:57304400-57331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr4:57305200-57311800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr4:57305800-57330400	Strong transcription	Fetal Thymus	thymus
42	chr4:57306200-57312200	Genic enhancers	HepG2	liver
43	chr4:57306200-57314000	Weak transcription	Fetal Intestine Small	intestine
44	chr4:57306200-57314600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr4:57306200-57330200	Weak transcription	Brain Angular Gyrus	brain
46	chr4:57306200-57332200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:57306400-57312800	Strong transcription	Primary B cells from cord blood	blood
48	chr4:57306600-57310000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:57306600-57323200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:57306600-57329400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links