Variant report

Variant	rs12049503
Chromosome Location	chr1:46021556-46021557
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
2	chr1:46020777..46023245-chr1:46030263..46032996,2	K562	blood:
3	chr1:46013953..46018760-chr1:46019151..46024741,9	K562	blood:
4	chr1:46015251..46018245-chr1:46018589..46025048,8	MCF-7	breast:
5	chr1:46013953..46019415-chr1:46020167..46024741,10	K562	blood:
6	chr1:46020234..46023064-chr1:46033814..46036863,3	K562	blood:

Variant related genes	Relation type
ENSG00000117450	Chromatin interaction
ENSG00000117448	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs1006216	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs10789471	0.80[JPT][hapmap]
rs10890330	0.90[CEU][hapmap];0.81[CHB][hapmap]
rs11211111	0.86[CEU][hapmap];0.81[CHB][hapmap];0.85[MEX][hapmap]
rs11211124	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.85[YRI][hapmap]
rs11211137	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211139	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211145	0.80[JPT][hapmap]
rs11211146	0.83[YRI][hapmap]
rs11211152	0.80[JPT][hapmap]
rs11211160	0.80[JPT][hapmap]
rs11211168	0.80[JPT][hapmap]
rs11211171	0.80[JPT][hapmap]
rs11211173	0.80[JPT][hapmap]
rs12023439	0.80[JPT][hapmap]
rs12024590	0.80[JPT][hapmap]
rs12029322	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.85[YRI][hapmap]
rs12046816	0.89[CEU][hapmap]
rs12077621	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494812	0.89[CEU][hapmap]
rs1771551	0.81[CEU][hapmap]
rs1826691	0.86[CEU][hapmap];0.81[CHB][hapmap];0.85[MEX][hapmap]
rs1972410	0.80[JPT][hapmap]
rs2055145	0.90[CEU][hapmap];0.81[CHB][hapmap];0.85[MEX][hapmap]
rs28719889	0.80[JPT][hapmap]
rs28890893	0.80[JPT][hapmap]
rs3014237	0.80[JPT][hapmap]
rs3014241	0.80[JPT][hapmap]
rs34673142	0.82[EUR][1000 genomes]
rs34768551	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3790582	0.86[CEU][hapmap];0.81[CHB][hapmap];0.85[MEX][hapmap]
rs3790585	0.82[CHB][hapmap];0.80[JPT][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs4633317	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs4660313	0.80[JPT][hapmap]
rs4660851	0.81[CEU][hapmap]
rs4660858	0.86[CEU][hapmap];0.81[CHB][hapmap];0.85[MEX][hapmap]
rs4660863	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.85[YRI][hapmap]
rs4660880	0.80[JPT][hapmap]
rs5015340	0.82[EUR][1000 genomes]
rs518216	0.90[GIH][hapmap]
rs61788356	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6657284	0.86[CEU][hapmap];0.81[CHB][hapmap];0.81[MEX][hapmap]
rs666720	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs6703748	0.80[JPT][hapmap]
rs713358	1.00[CEU][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs7531253	0.86[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap]
rs781226	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs781232	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs868351	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9727262	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
4	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12049503	MAST2	cis	cerebellum	SCAN
rs12049503	IPP	cis	lymphoblastoid	seeQTL
rs12049503	ST3GAL3	cis	parietal	SCAN
rs12049503	PRDX1	cis	Thyroid	GTEx
rs12049503	Hs.396207	cis	multi-tissue	Pritchard
rs12049503	IPP	cis	Lymphoblastoid	GTEx
rs12049503	TESK2	cis	Whole Blood	GTEx
rs12049503		cis	Lymphoblastoid	GTEx
rs12049503	C2orf49	trans	lymphoblastoid	RTeQTL
rs12049503	CYP4Z2P	cis	cerebellum	SCAN
rs12049503	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs12049503	GPBP1L1	cis	Lymphoblastoid	GTEx
rs12049503	MMACHC	cis	multi-tissue	Pritchard
rs12049503	IPP	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46017000-46025800	Weak transcription	Spleen	Spleen
2	chr1:46017400-46023000	Weak transcription	Psoas Muscle	Psoas
3	chr1:46017400-46027000	Weak transcription	Aorta	Aorta
4	chr1:46017400-46027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:46017800-46023000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:46017800-46023000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:46017800-46026800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:46017800-46026800	Weak transcription	Brain Substantia Nigra	brain
9	chr1:46017800-46026800	Weak transcription	HSMMtube	muscle
10	chr1:46017800-46027200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:46017800-46027400	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:46017800-46027400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:46017800-46027400	Weak transcription	Gastric	stomach
14	chr1:46017800-46032200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:46017800-46038800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:46018000-46027400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:46018000-46032200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:46018000-46038600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:46018200-46022000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:46018200-46022200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:46018200-46023000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:46018200-46037400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:46018400-46022000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:46018400-46022000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:46018400-46022000	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:46018400-46022000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:46018400-46022000	Strong transcription	K562	blood
28	chr1:46018400-46022200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:46018400-46022400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:46018400-46022800	Weak transcription	Fetal Heart	heart
31	chr1:46018400-46023000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:46018400-46023000	Weak transcription	Right Atrium	heart
33	chr1:46018400-46023000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:46018400-46023000	Weak transcription	Small Intestine	intestine
35	chr1:46018400-46024800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:46018400-46025600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:46018400-46025800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:46018400-46026600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:46018400-46026600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:46018400-46026800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:46018400-46026800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:46018400-46027200	Weak transcription	Fetal Lung	lung
43	chr1:46018400-46027400	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:46018400-46027400	Weak transcription	HUVEC	blood vessel
45	chr1:46018400-46029600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:46018400-46029800	Weak transcription	NHDF-Ad	bronchial
47	chr1:46018400-46032000	Weak transcription	Fetal Kidney	kidney
48	chr1:46018400-46032600	Weak transcription	Fetal Brain Male	brain
49	chr1:46018400-46036400	Strong transcription	Fetal Stomach	stomach
50	chr1:46018400-46036800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links