Variant report

Variant	rs1376781
Chromosome Location	chr2:187348984-187348985
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	TBP	chr2:187348972-187349383	HepG2	liver:	n/a	n/a
2	ARID3A	chr2:187348766-187349340	HepG2	liver:	n/a	n/a
3	MYBL2	chr2:187348711-187349695	HepG2	liver:	n/a	n/a
4	CHD1	chr2:187348914-187351966	GM12878	blood:	n/a	n/a
5	HEY1	chr2:187348720-187349524	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:187348798-187352419	GM12878	blood:	n/a	n/a
7	HNF4G	chr2:187348814-187349476	HepG2	liver:	n/a	chr2:187349277-187349291 chr2:187348959-187348967 chr2:187349273-187349295 chr2:187349435-187349447 chr2:187349282-187349294 chr2:187349278-187349290 chr2:187349432-187349450 chr2:187349434-187349448
8	TCF7L2	chr2:187348956-187349280	PANC-1	pancreas:	n/a	n/a
9	HEY1	chr2:187348891-187349466	HepG2	liver:	n/a	n/a
10	SPI1	chr2:187348898-187349227	GM12891	blood:	n/a	chr2:187349128-187349141
11	NFIC	chr2:187348695-187349442	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:187348502-187352426	GM12891	blood:	n/a	n/a
13	TBP	chr2:187348601-187349423	GM12878	blood:	n/a	n/a
14	NRF1	chr2:187348908-187349130	GM12878	blood:	n/a	n/a
15	NFIC	chr2:187348731-187349642	HepG2	liver:	n/a	n/a
16	NRF1	chr2:187348912-187348995	H1-hESC	embryonic stem cell:	n/a	n/a
17	TEAD4	chr2:187348424-187351525	HepG2	liver:	n/a	chr2:187349483-187349492
18	JUND	chr2:187348660-187349350	K562	blood:	n/a	n/a
19	MXI1	chr2:187348821-187348987	GM12878	blood:	n/a	n/a
20	EP300	chr2:187348744-187349502	HepG2	liver:	n/a	n/a
21	ZC3H11A	chr2:187348842-187349015	K562	blood:	n/a	n/a
22	REST	chr2:187348484-187349347	HL-60	blood:	n/a	n/a
23	SPI1	chr2:187348867-187349318	HL-60	blood:	n/a	chr2:187349128-187349141
24	TCF7L2	chr2:187348645-187349596	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:187348677-187349835	HepG2	liver:	n/a	n/a
26	POLR2A	chr2:187348950-187349105	K562	blood:	n/a	n/a
27	SPI1	chr2:187348823-187349368	HL-60	blood:	n/a	chr2:187349128-187349141
28	POLR2A	chr2:187348787-187349602	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187331928..187334444-chr2:187348052..187350692,2	MCF-7	breast:
2	chr2:187348777..187350496-chr2:187367699..187370297,2	MCF-7	breast:

Variant related genes	Relation type
ZC3H15	TF binding region
ENSG00000065548	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1026118	0.86[JPT][hapmap]
rs10931241	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12622084	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12993773	0.82[JPT][hapmap]
rs1597244	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16827774	0.80[ASN][1000 genomes]
rs16827790	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16827800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2029085	0.81[ASN][1000 genomes]
rs3754582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144823	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4606885	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667100	0.81[JPT][hapmap]
rs57550664	0.81[ASN][1000 genomes]
rs59228985	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61538288	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62198657	0.84[ASN][1000 genomes]
rs72893443	0.81[ASN][1000 genomes]
rs72893458	0.81[ASN][1000 genomes]
rs72893482	0.80[ASN][1000 genomes]
rs72895425	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72895447	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72895498	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72897378	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561955	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9636305	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking 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	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1376781	MST1	trans	brain	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187328000-187350400	Weak transcription	Pancreas	Pancrea
2	chr2:187339800-187349800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:187346400-187349200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:187346600-187350000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:187348000-187349000	Flanking Active TSS	GM12878-XiMat	blood
6	chr2:187348000-187349400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:187348200-187349000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:187348200-187349000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr2:187348200-187349400	Active TSS	Rectal Smooth Muscle	rectum
10	chr2:187348200-187350000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr2:187348200-187350000	Active TSS	Duodenum Mucosa	Duodenum
12	chr2:187348200-187352200	Active TSS	Colonic Mucosa	Colon
13	chr2:187348200-187353400	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr2:187348400-187349000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr2:187348400-187349000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:187348400-187349000	Flanking Active TSS	HepG2	liver
17	chr2:187348400-187349400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:187348400-187349800	Enhancers	Primary T cells from cord blood	blood
19	chr2:187348400-187350400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:187348600-187349000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:187348600-187349400	Active TSS	HMEC	breast
22	chr2:187348600-187349800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr2:187348600-187350000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr2:187348600-187350000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr2:187348600-187350000	Weak transcription	Ovary	ovary
26	chr2:187348600-187352600	Active TSS	Fetal Intestine Small	intestine
27	chr2:187348600-187353000	Active TSS	Fetal Intestine Large	intestine
28	chr2:187348800-187349000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:187348800-187349000	Enhancers	Fetal Kidney	kidney
30	chr2:187348800-187349000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr2:187348800-187349000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr2:187348800-187349200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:187348800-187349600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:187348800-187349600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:187348800-187349800	Enhancers	Primary B cells from cord blood	blood
36	chr2:187348800-187349800	Flanking Active TSS	NHEK	skin
37	chr2:187348800-187350000	Enhancers	Primary B cells from peripheral blood	blood
38	chr2:187348800-187350000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:187348800-187350000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:187348800-187350000	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr2:187348800-187350200	Enhancers	Stomach Mucosa	stomach
42	chr2:187348800-187350400	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr2:187348800-187350400	Flanking Active TSS	Dnd41	blood
44	chr2:187348800-187350600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:187348800-187352200	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr2:187348800-187353200	Active TSS	K562	blood

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