Variant report

Variant	rs10518872
Chromosome Location	chr15:57022183-57022184
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57020804..57022537-chr15:57050461..57051962,2	MCF-7	breast:
2	chr15:57021470..57024723-chr15:57024853..57027079,3	K562	blood:
3	chr15:57005760..57007990-chr15:57020400..57022198,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1087705	0.88[EUR][1000 genomes]
rs11071285	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11071286	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12437635	1.00[CEU][hapmap]
rs12437714	0.82[AMR][1000 genomes]
rs12437735	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12438377	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12438728	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12439116	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12439563	0.94[EUR][1000 genomes]
rs12439586	0.88[EUR][1000 genomes]
rs12439697	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12440006	0.94[EUR][1000 genomes]
rs12440725	1.00[CEU][hapmap]
rs12440891	1.00[CEU][hapmap]
rs12441746	0.89[EUR][1000 genomes]
rs12441769	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12441792	0.88[AMR][1000 genomes]
rs12442069	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12442630	0.82[AMR][1000 genomes]
rs12442662	1.00[CEU][hapmap]
rs12443178	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12903143	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12907983	0.94[EUR][1000 genomes]
rs1364541	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1564557	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1586022	0.83[EUR][1000 genomes]
rs1600829	0.94[EUR][1000 genomes]
rs1600831	0.89[EUR][1000 genomes]
rs1631905	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1647386	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1647391	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16977123	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17238859	0.82[EUR][1000 genomes]
rs17238880	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17238894	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17238901	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17819592	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17819616	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17819646	1.00[CEU][hapmap]
rs1834199	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2052641	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2161935	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2170461	0.83[EUR][1000 genomes]
rs2170462	0.88[EUR][1000 genomes]
rs2459565	0.88[EUR][1000 genomes]
rs2676178	0.88[EUR][1000 genomes]
rs2676181	0.88[EUR][1000 genomes]
rs2733231	0.83[EUR][1000 genomes]
rs2899599	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4287503	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4424865	0.82[AMR][1000 genomes]
rs4594195	0.83[EUR][1000 genomes]
rs4774869	0.83[EUR][1000 genomes]
rs4774885	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs480701	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493888	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7176472	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74015901	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8029710	0.85[EUR][1000 genomes]
rs966807	0.88[AMR][1000 genomes];0.83[EUR][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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv569576	chr15:57012816-57126917	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56971000-57023400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:56992600-57022600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:56993000-57024000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:56994000-57023800	Weak transcription	Fetal Kidney	kidney
5	chr15:56995800-57022200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:56996400-57022600	Weak transcription	NH-A	brain
7	chr15:56996800-57022600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:56997200-57022800	Weak transcription	Gastric	stomach
9	chr15:56997200-57023800	Weak transcription	Fetal Stomach	stomach
10	chr15:56998800-57023400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr15:56998800-57023800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:56999400-57023400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:57009400-57022800	Weak transcription	Right Atrium	heart
14	chr15:57009400-57024400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:57011000-57022200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:57011200-57022600	Weak transcription	Fetal Heart	heart
17	chr15:57011600-57022600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:57011600-57023400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:57011600-57024400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:57011600-57024400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:57011800-57022600	Weak transcription	HMEC	breast
22	chr15:57011800-57024000	Weak transcription	Aorta	Aorta
23	chr15:57012400-57022600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:57012400-57022600	Weak transcription	Osteobl	bone
25	chr15:57012400-57025000	Weak transcription	Spleen	Spleen
26	chr15:57012600-57022600	Weak transcription	NHEK	skin
27	chr15:57012600-57023000	Weak transcription	NHLF	lung
28	chr15:57012600-57023400	Weak transcription	Psoas Muscle	Psoas
29	chr15:57013000-57022800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:57013200-57022600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:57013400-57024200	Weak transcription	Ovary	ovary
32	chr15:57014000-57022400	Weak transcription	Brain Germinal Matrix	brain
33	chr15:57014200-57022800	Weak transcription	K562	blood
34	chr15:57015400-57022600	Weak transcription	HUVEC	blood vessel
35	chr15:57016400-57022600	Weak transcription	Stomach Mucosa	stomach
36	chr15:57016600-57022600	Weak transcription	Fetal Muscle Leg	muscle
37	chr15:57016800-57023400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr15:57017000-57022600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:57017400-57022200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:57017400-57022600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:57017400-57022800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr15:57017400-57022800	Weak transcription	Small Intestine	intestine
43	chr15:57017400-57023000	Weak transcription	Fetal Intestine Large	intestine
44	chr15:57017400-57023400	Weak transcription	Pancreas	Pancrea
45	chr15:57018000-57022200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:57018400-57022800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr15:57018600-57022600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:57018600-57023000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr15:57019000-57022600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr15:57019000-57022800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links