Variant report

Variant	rs1899819
Chromosome Location	chr15:41913668-41913669
allele	C/T
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	CHD2	chr15:41913484-41913867	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:41913190-41914644	MCF10A-Er-Src	breast:	n/a	n/a
3	USF1	chr15:41913059-41914564	SK-N-SH	brain:	n/a	chr15:41914208-41914224 chr15:41914260-41914269 chr15:41913676-41913685 chr15:41914258-41914267 chr15:41913674-41913687 chr15:41914259-41914268 chr15:41914253-41914274 chr15:41914216-41914232 chr15:41913677-41913686 chr15:41913676-41913685 chr15:41913670-41913691 chr15:41914259-41914268
4	POLR2A	chr15:41913013-41914509	Hela-S3	cervix:	n/a	n/a
5	YY1	chr15:41913149-41914316	HepG2	liver:	n/a	chr15:41914136-41914144 chr15:41914125-41914147 chr15:41913911-41913920 chr15:41914208-41914222 chr15:41914137-41914147 chr15:41913908-41913917 chr15:41913914-41913923 chr15:41913912-41913923 chr15:41914135-41914147 chr15:41913771-41913785
6	POLR2A	chr15:41913034-41914581	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr15:41913053-41914459	Hela-S3	cervix:	n/a	n/a
8	MXI1	chr15:41913197-41914469	HepG2	liver:	n/a	chr15:41913932-41913941
9	TAF1	chr15:41913075-41914292	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr15:41913174-41914459	Gliobla	brain:	n/a	n/a
11	CHD2	chr15:41913184-41914434	Hela-S3	cervix:	n/a	n/a
12	MAX	chr15:41913218-41914446	HepG2	liver:	n/a	chr15:41914258-41914269 chr15:41913676-41913685 chr15:41914239-41914249 chr15:41914183-41914199 chr15:41914192-41914201 chr15:41913906-41913916 chr15:41913675-41913686 chr15:41913809-41913818 chr15:41914259-41914268
13	ZBTB33	chr15:41913485-41913864	HepG2	liver:	n/a	n/a
14	STAT3	chr15:41913411-41913864	MCF10A-Er-Src	breast:	n/a	n/a
15	HEY1	chr15:41913133-41914250	HepG2	liver:	n/a	chr15:41913906-41913921 chr15:41913909-41913924
16	TAF1	chr15:41913172-41913836	PFSK-1	brain:	n/a	n/a
17	MAFF	chr15:41913581-41913875	HepG2	liver:	n/a	n/a
18	MYC	chr15:41913305-41913827	HUVEC	blood vessel:	n/a	chr15:41913676-41913685 chr15:41913675-41913686 chr15:41913809-41913818
19	MBD4	chr15:41913277-41913889	HepG2	liver:	n/a	n/a
20	SIN3AK20	chr15:41913373-41913688	A549	lung:	n/a	n/a
21	RUNX3	chr15:41913341-41913889	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:41913210-41913882	HepG2	liver:	n/a	n/a
23	CTCF	chr15:41913660-41913810	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr15:41913453-41913890	H1-hESC	embryonic stem cell:	n/a	n/a
25	TBP	chr15:41912869-41913809	Hela-S3	cervix:	n/a	n/a
26	MAX	chr15:41913240-41914536	A549	lung:	n/a	chr15:41914258-41914269 chr15:41913676-41913685 chr15:41914239-41914249 chr15:41914183-41914199 chr15:41914192-41914201 chr15:41913906-41913916 chr15:41913675-41913686 chr15:41913809-41913818 chr15:41914259-41914268
27	MYBL2	chr15:41913002-41913863	HepG2	liver:	n/a	n/a
28	POLR2A	chr15:41913333-41914495	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF7L2	chr15:41913145-41913795	PANC-1	pancreas:	n/a	n/a
30	MYC	chr15:41913337-41914331	HepG2	liver:	n/a	chr15:41914258-41914269 chr15:41913676-41913685 chr15:41914239-41914249 chr15:41914183-41914199 chr15:41914192-41914201 chr15:41913906-41913916 chr15:41913675-41913686 chr15:41913809-41913818 chr15:41914259-41914268
31	POLR2A	chr15:41913092-41914526	Hela-S3	cervix:	n/a	n/a
32	FOS	chr15:41913589-41913789	MCF10A-Er-Src	breast:	n/a	n/a
33	STAT3	chr15:41913416-41913841	MCF10A-Er-Src	breast:	n/a	n/a
34	MTA3	chr15:41913380-41913819	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:41913262-41913884	GM12878	blood:	n/a	n/a
36	ELK1	chr15:41913316-41914072	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr15:41913097-41914538	Hela-S3	cervix:	n/a	n/a
38	MYC	chr15:41913391-41913733	Hela-S3	cervix:	n/a	chr15:41913676-41913685 chr15:41913675-41913686
39	CEBPB	chr15:41913288-41913887	Hela-S3	cervix:	n/a	chr15:41913696-41913704
40	JUND	chr15:41913368-41914389	A549	lung:	n/a	chr15:41913914-41913923
41	MAX	chr15:41913078-41914497	SK-N-SH	brain:	n/a	chr15:41914258-41914269 chr15:41913676-41913685 chr15:41914239-41914249 chr15:41914183-41914199 chr15:41914192-41914201 chr15:41913906-41913916 chr15:41913675-41913686 chr15:41913809-41913818 chr15:41914259-41914268
42	REST	chr15:41913206-41914209	PANC-1	pancreas:	n/a	chr15:41913401-41913414 chr15:41914100-41914118 chr15:41914099-41914119 chr15:41914103-41914116 chr15:41914099-41914119 chr15:41913398-41913411 chr15:41914103-41914116
43	TCF12	chr15:41912832-41914554	A549	lung:	n/a	n/a
44	POLR2A	chr15:41913234-41914266	HEK293	kidney:	n/a	n/a
45	TCF12	chr15:41913268-41913680	A549	lung:	n/a	n/a
46	BACH1	chr15:41913613-41914119	H1-hESC	embryonic stem cell:	n/a	n/a
47	TAF1	chr15:41913219-41914145	HepG2	liver:	n/a	n/a
48	POLR2A	chr15:41913270-41913893	A549	lung:	n/a	n/a
49	BHLHE40	chr15:41913503-41913778	A549	lung:	n/a	chr15:41913676-41913685 chr15:41913674-41913687 chr15:41913677-41913686 chr15:41913676-41913685 chr15:41913670-41913691
50	MYBL2	chr15:41913060-41914285	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41913537..41914181-chr7:156685893..156686857,2	Hela-S3	cervix:
2	chr15:41913263..41914798-chr15:41951320..41953702,2	MCF-7	breast:
3	chr15:41913374..41914236-chr9:140135374..140136171,2	Hela-S3	cervix:
4	chr15:41913309..41913826-chr9:131445522..131446248,2	Hela-S3	cervix:
5	chr15:41900433..41903180-chr15:41911539..41913856,2	K562	blood:
6	chr15:41913003..41913826-chr6:34855469..34856066,2	Hela-S3	cervix:

Variant related genes	Relation type
MGA	TF binding region
ENSG00000174197	Chromatin interaction
ENSG00000064995	Chromatin interaction
ENSG00000119335	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000260926	Chromatin interaction
ENSG00000105983	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10152332	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10152364	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10775122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10775124	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1081022	1.00[CEU][hapmap]
rs11070345	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11070347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11632100	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11634840	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11639146	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11639249	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1197704	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[YRI][hapmap]
rs1197772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12148330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12441249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12900295	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12902548	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12916525	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16972089	0.92[CEU][hapmap]
rs1867416	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1867417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1880937	0.80[EUR][1000 genomes]
rs1880938	0.83[EUR][1000 genomes]
rs1899820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1918314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2141141	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2178004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2250964	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2577947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2577950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2577953	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2577958	0.81[EUR][1000 genomes]
rs2577959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2605570	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2695162	0.80[EUR][1000 genomes]
rs2695163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2695164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2695166	0.83[EUR][1000 genomes]
rs2695169	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2918051	0.83[EUR][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4244585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4270151	0.83[AMR][1000 genomes]
rs4371125	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924568	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924571	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62002067	0.83[AMR][1000 genomes]
rs62002069	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6493008	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6493010	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7164209	0.82[ASN][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7169668	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7176474	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7177232	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8027390	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8028886	0.81[AMR][1000 genomes]
rs8030179	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8034261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8038148	1.00[JPT][hapmap]
rs8038783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8039440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[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	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1899819	MGA	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41912600-41914400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:41912600-41915000	Active TSS	A549	lung
3	chr15:41912800-41914200	Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr15:41912800-41914200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr15:41912800-41914400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr15:41912800-41914400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr15:41912800-41914600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:41912800-41914600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr15:41912800-41914600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr15:41912800-41914600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:41912800-41914600	Flanking Active TSS	HepG2	liver
12	chr15:41912800-41914800	Active TSS	Brain Anterior Caudate	brain
13	chr15:41912800-41915000	Active TSS	Fetal Brain Female	brain
14	chr15:41913000-41913800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:41913000-41913800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr15:41913000-41913800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:41913000-41913800	Flanking Active TSS	HUVEC	blood vessel
18	chr15:41913000-41914000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:41913000-41914000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr15:41913000-41914000	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr15:41913000-41914000	Active TSS	Stomach Mucosa	stomach
22	chr15:41913000-41914200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr15:41913000-41914200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:41913000-41914200	Active TSS	Colon Smooth Muscle	Colon
25	chr15:41913000-41914200	Flanking Active TSS	Right Ventricle	heart
26	chr15:41913000-41914400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr15:41913000-41914400	Active TSS	Aorta	Aorta
28	chr15:41913000-41914400	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr15:41913000-41914600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:41913000-41914600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr15:41913000-41914600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:41913000-41914600	Active TSS	Brain Substantia Nigra	brain
33	chr15:41913000-41914600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr15:41913000-41914600	Active TSS	Ovary	ovary
35	chr15:41913000-41914600	Active TSS	Psoas Muscle	Psoas
36	chr15:41913000-41914600	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr15:41913000-41914600	Active TSS	Rectal Smooth Muscle	rectum
38	chr15:41913000-41914600	Active TSS	Right Atrium	heart
39	chr15:41913000-41914600	Active TSS	HSMM	muscle
40	chr15:41913000-41914600	Active TSS	HSMMtube	muscle
41	chr15:41913000-41914800	Active TSS	Brain Cingulate Gyrus	brain
42	chr15:41913200-41913800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:41913200-41913800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr15:41913200-41913800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:41913200-41913800	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr15:41913200-41913800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
47	chr15:41913200-41913800	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr15:41913200-41913800	Flanking Active TSS	Spleen	Spleen
49	chr15:41913200-41913800	Flanking Active TSS	GM12878-XiMat	blood
50	chr15:41913200-41913800	Flanking Active TSS	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links