Variant report

Variant	rs12124929
Chromosome Location	chr1:184710178-184710179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184709738..184712321-chr1:184713250..184716697,3	K562	blood:
2	chr1:184708584..184710764-chr1:184716187..184718399,2	MCF-7	breast:
3	chr1:184708496..184710858-chr1:184733789..184736072,2	K562	blood:
4	chr1:184703854..184706366-chr1:184709752..184714206,4	K562	blood:
5	chr1:184708169..184713415-chr1:184713456..184716461,4	MCF-7	breast:
6	chr1:184708973..184712904-chr1:184713895..184716754,5	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1061508	1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap]
rs1062994	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911631	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10911633	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911634	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911636	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911644	0.82[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911645	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11808675	0.83[EUR][1000 genomes]
rs12031028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12032144	0.80[AMR][1000 genomes]
rs12071631	0.87[GIH][hapmap]
rs12126231	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12131285	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12133128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137438	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12184284	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12567225	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12567226	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2024767	0.87[GIH][hapmap]
rs2064605	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2333715	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2333716	0.87[GIH][hapmap]
rs2877994	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3736757	0.87[GIH][hapmap]
rs3895196	0.81[GIH][hapmap]
rs4233120	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4651230	0.82[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs481215	0.82[ASW][hapmap]
rs484847	0.82[ASW][hapmap]
rs543912	1.00[ASW][hapmap]
rs549088	0.82[ASW][hapmap]
rs641337	1.00[ASW][hapmap]
rs6662416	0.81[AFR][1000 genomes]
rs6663178	0.85[GIH][hapmap]
rs67359172	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs726427	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs861574	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs861575	0.83[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs861576	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs861577	0.84[EUR][1000 genomes]
rs861578	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs861581	1.00[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs861583	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9425338	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9425340	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9425343	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9425632	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9425634	0.90[ASN][1000 genomes]
rs971081	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS 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	69 gene(s)	inside rSNPs	diseases
3	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1009529	chr1:184663898-184731215	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1001244	chr1:184667198-184715195	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1849889	chr1:184667371-184718601	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv872584	chr1:184678290-184716457	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12124929	EDEM3	cis	Esophagus Muscularis	GTEx
rs12124929	FAM129A	cis	cerebellum	SCAN
rs12124929	C1orf200	trans	cerebellum	SCAN
rs12124929	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs12124929	PRG4	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184654000-184710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:184674600-184723000	Weak transcription	Aorta	Aorta
3	chr1:184677600-184723200	Weak transcription	Lung	lung
4	chr1:184678800-184710800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:184685000-184721800	Weak transcription	Fetal Heart	heart
6	chr1:184685400-184722800	Weak transcription	Ovary	ovary
7	chr1:184685600-184711200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:184685600-184714400	Weak transcription	Brain Substantia Nigra	brain
9	chr1:184685600-184721000	Weak transcription	Right Ventricle	heart
10	chr1:184685600-184722600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:184685800-184715000	Weak transcription	Small Intestine	intestine
12	chr1:184686200-184722600	Weak transcription	Brain Germinal Matrix	brain
13	chr1:184686400-184715600	Weak transcription	Colonic Mucosa	Colon
14	chr1:184688800-184714200	Weak transcription	Fetal Brain Male	brain
15	chr1:184690400-184721800	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:184695200-184715400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:184695400-184714800	Weak transcription	HepG2	liver
18	chr1:184698200-184722800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:184698400-184715000	Weak transcription	Fetal Lung	lung
20	chr1:184699400-184715200	Weak transcription	HUVEC	blood vessel
21	chr1:184699800-184710800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:184699800-184711600	Weak transcription	Gastric	stomach
23	chr1:184699800-184711600	Weak transcription	Thymus	Thymus
24	chr1:184699800-184722200	Weak transcription	Fetal Stomach	stomach
25	chr1:184700000-184711000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:184700000-184711600	Weak transcription	Psoas Muscle	Psoas
27	chr1:184701000-184714400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:184701600-184721800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:184701800-184715000	Weak transcription	Brain Anterior Caudate	brain
30	chr1:184702000-184712000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:184702200-184712000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:184702200-184714800	Weak transcription	Brain Angular Gyrus	brain
33	chr1:184702200-184721800	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:184702200-184721800	Weak transcription	NH-A	brain
35	chr1:184702200-184722200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:184702600-184712200	Weak transcription	HMEC	breast
37	chr1:184702600-184712600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:184702600-184715000	Weak transcription	Primary B cells from cord blood	blood
39	chr1:184703000-184715400	Weak transcription	HSMMtube	muscle
40	chr1:184703200-184721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:184703200-184722800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:184703400-184710800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:184703400-184714200	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:184703400-184721400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:184703600-184711000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:184703600-184715000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:184703600-184715200	Weak transcription	Fetal Intestine Small	intestine
48	chr1:184703600-184720800	Weak transcription	Pancreas	Pancrea
49	chr1:184704400-184714800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:184704600-184721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links