Variant report

Variant	rs2476153
Chromosome Location	chr1:47113911-47113912
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:47113840-47113918	GM13976	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47107881..47110216-chr1:47113427..47115932,2	K562	blood:

Variant related genes	Relation type
ATPAF1	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10890410	0.88[ASN][1000 genomes]
rs10890414	0.87[ASN][1000 genomes]
rs11211332	1.00[EUR][1000 genomes]
rs11211343	0.87[ASN][1000 genomes]
rs11801744	0.87[ASN][1000 genomes]
rs12562113	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12566278	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568734	0.87[ASN][1000 genomes]
rs1258055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1258058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258063	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1258064	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258065	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258066	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258068	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258072	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1268714	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1273237	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13374909	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1745376	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1933932	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2146560	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2181412	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241863	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2241864	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2439442	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476155	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476157	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2476159	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2486160	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486162	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011290	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3766218	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766220	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766221	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3766222	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766223	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56771521	0.87[ASN][1000 genomes]
rs57495753	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582269	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs582323	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs582760	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs583649	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58678760	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59479990	0.87[ASN][1000 genomes]
rs596794	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs597221	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604233	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604264	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs611919	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs629412	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631368	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631840	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636082	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs636122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636424	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648822	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs654544	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs655369	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs657166	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs669647	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs673134	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs675731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678466	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs683585	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs689300	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs723333	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724309	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72896683	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72900715	0.87[ASN][1000 genomes]
rs736188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9094	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1007280	chr1:47088116-47129588	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47083200-47115000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:47090200-47121400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:47094600-47119200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:47101600-47130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:47101800-47115000	Weak transcription	Dnd41	blood
8	chr1:47101800-47115200	Weak transcription	Gastric	stomach
9	chr1:47101800-47119000	Weak transcription	Colonic Mucosa	Colon
10	chr1:47101800-47121200	Weak transcription	HUVEC	blood vessel
11	chr1:47102000-47115000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:47102000-47122400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:47102400-47121400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:47103000-47115200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:47103000-47115200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:47103000-47132800	Weak transcription	Spleen	Spleen
17	chr1:47105000-47132800	Weak transcription	Stomach Mucosa	stomach
18	chr1:47105800-47115200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:47106800-47114600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:47107000-47115200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:47107800-47115200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:47108200-47123400	Weak transcription	K562	blood
23	chr1:47108800-47115200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:47109000-47115400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:47109200-47115000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:47109200-47115200	Weak transcription	Esophagus	oesophagus
27	chr1:47109200-47115200	Weak transcription	HSMMtube	muscle
28	chr1:47109400-47129800	Weak transcription	Pancreas	Pancrea
29	chr1:47109400-47132600	Weak transcription	Hela-S3	cervix
30	chr1:47109600-47114000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:47109600-47114800	Weak transcription	NHLF	lung
32	chr1:47109600-47115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:47109600-47115000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:47109600-47115200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:47109600-47115200	Weak transcription	Aorta	Aorta
36	chr1:47109600-47115200	Weak transcription	Psoas Muscle	Psoas
37	chr1:47109600-47115400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:47109600-47123400	Weak transcription	NH-A	brain
39	chr1:47109600-47132600	Weak transcription	HMEC	breast
40	chr1:47109800-47116600	Strong transcription	Left Ventricle	heart
41	chr1:47109800-47123200	Weak transcription	HepG2	liver
42	chr1:47110200-47115200	Weak transcription	A549	lung
43	chr1:47112000-47115400	Strong transcription	Brain Anterior Caudate	brain
44	chr1:47112200-47114000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:47112200-47114200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:47112200-47125600	Strong transcription	Liver	Liver
47	chr1:47112400-47114200	Strong transcription	Primary B cells from cord blood	blood
48	chr1:47112400-47115200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:47112400-47116200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:47112400-47116600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links