Variant report

Variant	rs2554351
Chromosome Location	chr15:52132475-52132476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52130556..52132790-chr15:52135069..52138067,2	MCF-7	breast:
2	chr15:52131004..52134205-chr15:52136724..52139101,4	K562	blood:
3	chr15:52131973..52134112-chr20:52194712..52196799,2	MCF-7	breast:
4	chr15:52132428..52137559-chr15:52138263..52141048,4	MCF-7	breast:
5	chr15:52129040..52133421-chr15:52134334..52139621,6	K562	blood:
6	chr15:52131773..52132639-chr8:88082437..88083070,2	MCF-7	breast:
7	chr15:52132092..52134106-chr15:52134200..52135846,2	MCF-7	breast:

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs1025185	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10519323	1.00[EUR][1000 genomes]
rs10519325	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519326	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438469	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442283	1.00[EUR][1000 genomes]
rs1378891	1.00[EUR][1000 genomes]
rs1426085	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1426086	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649047	1.00[EUR][1000 genomes]
rs17649178	1.00[EUR][1000 genomes]
rs17649255	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649391	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649692	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17649801	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17705530	1.00[EUR][1000 genomes]
rs17705649	1.00[EUR][1000 genomes]
rs17705685	1.00[EUR][1000 genomes]
rs17705889	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17706076	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052707	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2162224	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263946	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2436663	0.87[AFR][1000 genomes]
rs2436664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470609	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2470613	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554309	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554310	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554311	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554312	0.81[AFR][1000 genomes]
rs2554317	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554318	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554319	0.81[AFR][1000 genomes]
rs2554320	0.81[AFR][1000 genomes]
rs2554321	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554323	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554324	0.87[AFR][1000 genomes]
rs2554325	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554326	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554329	0.87[AFR][1000 genomes]
rs2554330	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554333	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554341	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2554344	0.87[AFR][1000 genomes]
rs2554352	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570218	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570219	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570220	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570221	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570222	0.81[AFR][1000 genomes]
rs2570223	0.81[AFR][1000 genomes]
rs2570225	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570227	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570232	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2570234	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2570242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570244	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570246	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2570247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570259	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570262	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2570266	0.81[AFR][1000 genomes]
rs2570267	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570270	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570273	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2570274	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593165	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593171	0.81[AFR][1000 genomes]
rs2593172	0.81[AFR][1000 genomes]
rs2593175	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593176	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593180	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623248	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623253	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2623257	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623260	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623261	0.95[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2623264	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623267	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623268	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623273	0.87[AFR][1000 genomes]
rs2623274	0.87[AFR][1000 genomes]
rs2623275	0.87[AFR][1000 genomes]
rs2623277	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623278	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623287	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623290	0.81[AFR][1000 genomes]
rs2623293	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2899483	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2916174	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959297	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2959303	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099570	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34407523	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794533	1.00[EUR][1000 genomes]
rs3794537	1.00[EUR][1000 genomes]
rs4774600	1.00[EUR][1000 genomes]
rs4774601	1.00[EUR][1000 genomes]
rs4775979	1.00[EUR][1000 genomes]
rs4775987	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775988	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775989	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166322	1.00[EUR][1000 genomes]
rs7170429	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7170700	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7173661	1.00[EUR][1000 genomes]
rs7179139	1.00[EUR][1000 genomes]
rs73411105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013606	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8024441	1.00[EUR][1000 genomes]
rs8026507	1.00[EUR][1000 genomes]
rs8027426	1.00[EUR][1000 genomes]
rs8042310	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs919056	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs919057	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919058	0.87[AFR][1000 genomes]
rs990666	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52123000-52134000	Weak transcription	Pancreas	Pancrea
2	chr15:52123400-52133600	Weak transcription	Colonic Mucosa	Colon
3	chr15:52123600-52140000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr15:52124200-52134600	Weak transcription	HSMM	muscle
5	chr15:52124200-52134800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:52124200-52135000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:52124200-52135000	Weak transcription	Aorta	Aorta
8	chr15:52124200-52135400	Weak transcription	Thymus	Thymus
9	chr15:52125000-52137600	Weak transcription	Lung	lung
10	chr15:52129000-52136000	Enhancers	Fetal Lung	lung
11	chr15:52129000-52136600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr15:52129000-52140200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:52129200-52139800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr15:52129400-52140000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:52130000-52133000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr15:52130000-52133200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:52130000-52155000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr15:52130200-52133200	Weak transcription	Fetal Intestine Small	intestine
19	chr15:52130200-52133600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:52130200-52134400	Weak transcription	Brain Hippocampus Middle	brain
21	chr15:52130200-52134600	Weak transcription	Psoas Muscle	Psoas
22	chr15:52130200-52135000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:52130400-52133000	Weak transcription	NHDF-Ad	bronchial
24	chr15:52130400-52133200	Weak transcription	Fetal Intestine Large	intestine
25	chr15:52130400-52133600	Weak transcription	HMEC	breast
26	chr15:52130400-52134400	Weak transcription	NH-A	brain
27	chr15:52130400-52134600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:52130400-52134600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:52130400-52134600	Weak transcription	HSMMtube	muscle
30	chr15:52130400-52134800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr15:52130400-52134800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:52130400-52134800	Weak transcription	Osteobl	bone
33	chr15:52130400-52135000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:52130400-52135000	Weak transcription	Brain Substantia Nigra	brain
35	chr15:52130400-52135200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:52130400-52137000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:52130400-52137600	Weak transcription	Placenta	Placenta
38	chr15:52130600-52133000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:52130600-52133600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:52130600-52133600	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr15:52130600-52133600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:52130600-52134800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:52130600-52134800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:52130600-52134800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:52130600-52135000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:52130600-52135600	Weak transcription	Brain Anterior Caudate	brain
47	chr15:52130600-52136200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr15:52130800-52133000	Weak transcription	Hela-S3	cervix
49	chr15:52130800-52133000	Weak transcription	K562	blood
50	chr15:52130800-52133600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links