Variant report

Variant	rs1124836
Chromosome Location	chr2:85833046-85833047
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	POLR2A	chr2:85832471-85833064	PANC-1	pancreas:	n/a	n/a
2	NFIC	chr2:85832753-85833326	HepG2	liver:	n/a	chr2:85833007-85833023
3	FOXA1	chr2:85832824-85833376	HepG2	liver:	n/a	n/a
4	HEY1	chr2:85832891-85833577	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:85831593-85833831	Hela-S3	cervix:	n/a	n/a
6	FOXA1	chr2:85832755-85833320	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:85832420-85833667	PANC-1	pancreas:	n/a	n/a
8	TEAD4	chr2:85832499-85833419	HepG2	liver:	n/a	chr2:85833245-85833254 chr2:85832722-85832731 chr2:85832962-85832971
9	NFIC	chr2:85832631-85833295	ECC-1	luminal epithelium:	n/a	chr2:85833007-85833023
10	POLR2A	chr2:85833016-85833524	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr2:85832703-85833582	SK-N-SH	brain:	n/a	n/a
12	FOXA1	chr2:85832881-85833259	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:85832564-85835446	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:85830971-85836753	K562	blood:	n/a	n/a
15	POLR2A	chr2:85832860-85833299	HepG2	liver:	n/a	n/a
16	FOXA1	chr2:85832730-85833389	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:85832962-85833721	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:85832593-85833574	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr2:85832634-85833870	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:85832735-85833591	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:85832603-85833529	GM12878	blood:	n/a	n/a
22	FOXA2	chr2:85832822-85833285	HepG2	liver:	n/a	n/a
23	NFIC	chr2:85832728-85833498	HepG2	liver:	n/a	chr2:85833007-85833023
24	POLR2A	chr2:85832720-85833463	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr2:85832747-85833362	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr2:85832408-85833809	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr2:85832508-85833778	K562	blood:	n/a	n/a
28	NFIC	chr2:85832669-85833352	ECC-1	luminal epithelium:	n/a	chr2:85833007-85833023
29	POLR2A	chr2:85832432-85833659	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr2:85832948-85833046	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr2:85832860-85833600	K562	blood:	n/a	n/a
32	POLR2A	chr2:85831284-85835767	HepG2	liver:	n/a	n/a
33	NFIC	chr2:85832684-85833368	SK-N-SH	brain:	n/a	chr2:85833007-85833023
34	JUND	chr2:85832779-85833289	HepG2	liver:	n/a	chr2:85833176-85833185
35	CEBPB	chr2:85833001-85833305	IMR90	lung:	n/a	n/a
36	MYBL2	chr2:85832724-85833503	HepG2	liver:	n/a	n/a
37	EP300	chr2:85832755-85833288	HepG2	liver:	n/a	chr2:85833050-85833064 chr2:85833124-85833134

No.	Distal block	Cell Line	Cell type
1	chr2:85788277..85790552-chr2:85828325..85833718,7	MCF-7	breast:
2	chr2:85786409..85789816-chr2:85832001..85837582,5	MCF-7	breast:
3	chr2:85616830..85619034-chr2:85831650..85834132,2	MCF-7	breast:
4	chr2:85764113..85767301-chr2:85832066..85833710,3	MCF-7	breast:
5	chr2:85621094..85626014-chr2:85830124..85833920,6	MCF-7	breast:
6	chr2:85765201..85768026-chr2:85832043..85835271,3	K562	blood:
7	chr2:85804054..85806144-chr2:85831864..85833379,2	K562	blood:

Variant related genes	Relation type
TMEM150A	TF binding region
ENSG00000168906	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000115486	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10180770	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10182351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10190428	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10191726	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10302	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1044158	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs13383605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13414982	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs13418207	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs14242	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1446669	0.84[JPT][hapmap]
rs1562322	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1992151	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2028898	0.84[JPT][hapmap]
rs2043675	0.84[JPT][hapmap]
rs2118176	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2232747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2232748	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2232750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2592551	0.84[JPT][hapmap]
rs3024831	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs3198089	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755009	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755010	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755011	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3827550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6547629	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs6643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6733550	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs6743051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs699664	0.84[JPT][hapmap]
rs762684	0.84[JPT][hapmap]

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	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1124836	VAMP8	cis	lymphoblastoid	seeQTL
rs1124836	ENSG00000168887	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85830600-85834800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:85830600-85835800	Enhancers	Fetal Heart	heart
3	chr2:85830600-85836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:85830800-85833400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr2:85830800-85833600	Enhancers	Stomach Mucosa	stomach
6	chr2:85830800-85835600	Enhancers	Right Atrium	heart
7	chr2:85830800-85838200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:85830800-85838200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:85830800-85838600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:85831000-85833200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr2:85831000-85833400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:85831000-85833600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr2:85831200-85833200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:85831200-85833400	Enhancers	Fetal Intestine Large	intestine
15	chr2:85831200-85833600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:85831200-85833600	Enhancers	Adipose Nuclei	Adipose
17	chr2:85831200-85833600	Enhancers	Brain Anterior Caudate	brain
18	chr2:85831200-85833600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:85831200-85833600	Enhancers	NHDF-Ad	bronchial
20	chr2:85831200-85833800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:85831200-85833800	Enhancers	Brain Hippocampus Middle	brain
22	chr2:85831200-85834600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:85831200-85834600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:85831200-85834600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:85831200-85834800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:85831200-85835800	Weak transcription	Small Intestine	intestine
27	chr2:85831400-85833200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:85831400-85833400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:85831400-85833400	Genic enhancers	Fetal Intestine Small	intestine
30	chr2:85831400-85833600	Enhancers	Brain Angular Gyrus	brain
31	chr2:85831400-85833800	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:85831400-85834000	Weak transcription	Primary B cells from cord blood	blood
33	chr2:85831400-85834400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:85831400-85834600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:85831400-85834600	Enhancers	Placenta	Placenta
36	chr2:85831400-85834600	Weak transcription	GM12878-XiMat	blood
37	chr2:85831400-85834800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:85831400-85836000	Genic enhancers	HSMM	muscle
39	chr2:85831600-85833600	Enhancers	Aorta	Aorta
40	chr2:85831600-85833600	Genic enhancers	K562	blood
41	chr2:85831600-85833800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:85831600-85835200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:85831800-85833200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:85831800-85833200	Weak transcription	Thymus	Thymus
45	chr2:85831800-85833600	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr2:85831800-85833600	Flanking Active TSS	Osteobl	bone
47	chr2:85831800-85833800	Genic enhancers	Fetal Muscle Leg	muscle
48	chr2:85832000-85833200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr2:85832000-85833200	Weak transcription	Gastric	stomach
50	chr2:85832000-85833200	Enhancers	NH-A	brain

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