Variant report

Variant	rs1649890
Chromosome Location	chr2:231337546-231337547
allele	A/C
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	BCLAF1	chr2:231335664-231338387	GM12878	blood:	n/a	chr2:231335975-231335984 chr2:231338274-231338283
2	STAT3	chr2:231337325-231337684	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr2:231337307-231337708	MCF10A-Er-Src	breast:	n/a	chr2:231337529-231337537 chr2:231337527-231337539
4	POLR2A	chr2:231337342-231337848	GM12891	blood:	n/a	n/a
5	FOXM1	chr2:231336923-231338541	GM12878	blood:	n/a	n/a
6	STAT3	chr2:231337381-231337689	MCF10A-Er-Src	breast:	n/a	n/a
7	JUND	chr2:231337206-231337839	HCT-116	colon:	n/a	chr2:231337529-231337537 chr2:231337527-231337539
8	ATF2	chr2:231336631-231337934	GM12878	blood:	n/a	n/a
9	RUNX3	chr2:231337015-231338005	GM12878	blood:	n/a	n/a
10	BCL3	chr2:231336969-231338509	GM12878	blood:	n/a	chr2:231338274-231338283
11	POLR2A	chr2:231337383-231337842	U87	brain:	n/a	n/a
12	CEBPB	chr2:231337229-231337878	HCT-116	colon:	n/a	n/a
13	CREB1	chr2:231336974-231338588	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:231335276-231338471	GM12892	blood:	n/a	n/a
15	NFIC	chr2:231336910-231337819	GM12878	blood:	n/a	n/a
16	EP300	chr2:231337447-231337647	GM12878	blood:	n/a	n/a
17	STAT5A	chr2:231337057-231337738	GM12878	blood:	n/a	n/a
18	IKZF1	chr2:231337138-231337825	GM12878	blood:	n/a	n/a
19	FOXM1	chr2:231337017-231338061	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:231337332-231337686	HCT-116	colon:	n/a	n/a
21	BCLAF1	chr2:231337169-231337854	GM12878	blood:	n/a	n/a
22	PML	chr2:231335735-231338638	GM12878	blood:	n/a	n/a
23	STAT5A	chr2:231336899-231338564	GM12878	blood:	n/a	chr2:231338212-231338224
24	POLR2A	chr2:231337246-231338526	GM12891	blood:	n/a	n/a
25	POU2F2	chr2:231337338-231337740	GM12891	blood:	n/a	n/a
26	FOS	chr2:231337307-231337710	MCF10A-Er-Src	breast:	n/a	chr2:231337529-231337537 chr2:231337527-231337539
27	POLR2A	chr2:231335747-231338559	GM12892	blood:	n/a	n/a
28	POLR2A	chr2:231337444-231337791	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:231337377-231337842	U87	brain:	n/a	n/a
30	CEBPB	chr2:231337394-231337721	Hela-S3	cervix:	n/a	n/a
31	SP1	chr2:231337359-231337896	HCT-116	colon:	n/a	n/a
32	POLR2A	chr2:231335449-231339009	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:231337492-231337639	GM12878	blood:	n/a	n/a
34	NFIC	chr2:231336886-231338547	GM12878	blood:	n/a	n/a
35	MYC	chr2:231337433-231337690	MCF10A-Er-Src	breast:	n/a	n/a
36	IRF4	chr2:231337232-231337736	GM12878	blood:	n/a	n/a
37	POLR2A	chr2:231335649-231338240	K562	blood:	n/a	n/a
38	FOSL1	chr2:231337383-231337822	HCT-116	colon:	n/a	chr2:231337529-231337537 chr2:231337527-231337539
39	BHLHE40	chr2:231337268-231337612	GM12878	blood:	n/a	n/a
40	JUND	chr2:231337387-231337691	K562	blood:	n/a	chr2:231337529-231337537 chr2:231337527-231337539
41	MTA3	chr2:231336923-231338491	GM12878	blood:	n/a	n/a
42	SMC3	chr2:231337394-231337724	GM12878	blood:	n/a	n/a
43	MTA3	chr2:231335661-231338637	GM12878	blood:	n/a	n/a
44	RUNX3	chr2:231336980-231337787	GM12878	blood:	n/a	n/a
45	POLR2A	chr2:231337441-231337699	GM12878	blood:	n/a	n/a
46	NFATC1	chr2:231336907-231338818	GM12878	blood:	n/a	n/a
47	CUX1	chr2:231337336-231337715	GM12878	blood:	n/a	n/a
48	SPI1	chr2:231336945-231337664	GM12891	blood:	n/a	chr2:231337209-231337222 chr2:231337386-231337399 chr2:231337215-231337224 chr2:231337386-231337399 chr2:231337208-231337221 chr2:231337387-231337400 chr2:231337208-231337221
49	WRNIP1	chr2:231337543-231337695	GM12878	blood:	n/a	n/a
50	MYC	chr2:231337400-231337690	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SP100	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1050224	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1615190	0.99[ASN][1000 genomes]
rs1622283	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1622822	0.99[ASN][1000 genomes]
rs1622980	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1649869	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1649884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1649929	0.99[ASN][1000 genomes]
rs2219811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4972955	0.97[ASN][1000 genomes]
rs56136530	0.84[AFR][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	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv584672	chr2:231289976-231348888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1649890	SP100	Cis_1M	lymphoblastoid	RTeQTL
rs1649890	DNAJB3	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231288800-231356000	Weak transcription	Stomach Mucosa	stomach
2	chr2:231301800-231345000	Weak transcription	A549	lung
3	chr2:231321800-231338600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:231322200-231340200	Strong transcription	Liver	Liver
5	chr2:231322600-231338200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:231323400-231337600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:231323800-231337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:231325800-231338400	Strong transcription	Left Ventricle	heart
9	chr2:231325800-231338600	Strong transcription	Lung	lung
10	chr2:231325800-231338800	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:231328200-231338400	Strong transcription	Fetal Muscle Leg	muscle
12	chr2:231329600-231343800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:231331200-231338400	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr2:231332000-231345200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:231332200-231338200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:231332400-231344400	Weak transcription	Gastric	stomach
17	chr2:231332800-231339200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:231333400-231339800	Genic enhancers	Primary B cells from cord blood	blood
19	chr2:231334200-231356000	Weak transcription	Fetal Intestine Small	intestine
20	chr2:231334600-231340000	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr2:231334800-231358400	Weak transcription	Fetal Stomach	stomach
22	chr2:231335000-231337600	Strong transcription	Primary hematopoietic stem cells	blood
23	chr2:231335000-231344400	Weak transcription	Aorta	Aorta
24	chr2:231335000-231359000	Weak transcription	NHLF	lung
25	chr2:231335600-231339000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
26	chr2:231335600-231340200	Weak transcription	Fetal Intestine Large	intestine
27	chr2:231335600-231344600	Weak transcription	Pancreas	Pancrea
28	chr2:231336000-231343800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:231336000-231344400	Weak transcription	Esophagus	oesophagus
30	chr2:231336000-231356000	Weak transcription	NHDF-Ad	bronchial
31	chr2:231336200-231342200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:231336200-231344400	Weak transcription	HSMMtube	muscle
33	chr2:231336400-231337600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:231336400-231337800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:231336400-231338000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:231336400-231338400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:231336400-231339200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:231336400-231339400	Weak transcription	Psoas Muscle	Psoas
39	chr2:231336400-231343800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:231336400-231345200	Weak transcription	Small Intestine	intestine
41	chr2:231336400-231363400	Weak transcription	Fetal Lung	lung
42	chr2:231336600-231337600	Weak transcription	Dnd41	blood
43	chr2:231336600-231337800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:231336600-231338200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:231336600-231338400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:231336600-231339000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr2:231336600-231340000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:231336600-231342200	Weak transcription	Ovary	ovary
49	chr2:231336600-231344200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:231336600-231345000	Weak transcription	Spleen	Spleen

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