Variant report

Variant	rs510293
Chromosome Location	chr1:225732239-225732240
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225726335..225728702-chr1:225730205..225734666,5	MCF-7	breast:
2	chr1:225725972..225727966-chr1:225729747..225732375,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10753406	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10799311	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10799314	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10799316	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs10799317	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10799318	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10915828	0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[YRI][hapmap]
rs10915830	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10915833	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10915834	0.92[EUR][1000 genomes]
rs10915837	0.81[ASN][1000 genomes]
rs10915839	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10915847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584675	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12028305	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1222440	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs12729655	0.81[ASN][1000 genomes]
rs2639703	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2639712	0.84[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs2639716	0.84[EUR][1000 genomes]
rs2657564	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2657569	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs2840958	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2840967	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs2840968	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs3820226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856156	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653643	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs476540	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs487591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs498350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511649	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs516249	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs551996	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs554744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs554992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs561656	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6426076	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6668770	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6676201	0.81[ASN][1000 genomes]
rs6678806	0.81[ASN][1000 genomes]
rs6697783	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs6702555	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7515907	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7515963	0.81[ASN][1000 genomes]
rs7524766	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7540181	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7541598	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7555139	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555553	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs812523	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs947034	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9804142	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers 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 target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs510293	RP11-496N12.9	cis	Thyroid	GTEx
rs510293	PYCR2	cis	cerebellum	SCAN
rs510293	DUSP10	cis	parietal	SCAN
rs510293	MIXL1	cis	cerebellum	SCAN
rs510293	USP10	trans	brain	seeQTL
rs510293	LBR	cis	Artery Tibial	GTEx
rs510293	C1orf58	cis	parietal	SCAN
rs510293	ENAH	cis	normal skin	skin_eQTL
rs510293	DHX33	trans	multi-tissue	Pritchard

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
2	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
3	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225707200-225755000	Weak transcription	Gastric	stomach
5	chr1:225717600-225744400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:225717800-225744400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:225717800-225745000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:225717800-225747400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:225717800-225747400	Weak transcription	Fetal Stomach	stomach
10	chr1:225717800-225758200	Weak transcription	HepG2	liver
11	chr1:225718400-225732600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:225718400-225756400	Weak transcription	NHLF	lung
13	chr1:225721600-225735200	Weak transcription	HSMM	muscle
14	chr1:225722800-225747600	Weak transcription	Fetal Intestine Small	intestine
15	chr1:225723200-225739600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:225723400-225735200	Weak transcription	NH-A	brain
17	chr1:225726800-225732800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:225726800-225744000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:225727200-225739200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:225727400-225736200	Weak transcription	HSMMtube	muscle
21	chr1:225727400-225737800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:225727400-225744400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:225727400-225747600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:225727400-225747600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:225727600-225732800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:225727600-225735400	Weak transcription	Brain Anterior Caudate	brain
27	chr1:225727600-225737600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:225727600-225753600	Weak transcription	NHEK	skin
29	chr1:225727800-225735800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:225728000-225753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:225728200-225735200	Weak transcription	A549	lung
32	chr1:225728400-225735000	Weak transcription	Fetal Lung	lung
33	chr1:225728400-225735400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:225728800-225737400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:225728800-225739200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:225730000-225732600	Weak transcription	Aorta	Aorta
37	chr1:225730000-225744400	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:225730200-225733800	Weak transcription	Left Ventricle	heart
39	chr1:225730200-225735000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:225730200-225735200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:225730200-225736600	Weak transcription	Right Atrium	heart
42	chr1:225730200-225737600	Weak transcription	Ovary	ovary
43	chr1:225730200-225747600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:225730200-225753400	Weak transcription	NHDF-Ad	bronchial
45	chr1:225730200-225753600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:225730400-225737200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:225730400-225744000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:225730600-225737400	Weak transcription	Right Ventricle	heart
49	chr1:225730600-225747600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links