Variant report

Variant	rs1649887
Chromosome Location	chr2:231336744-231336745
allele	A/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	BCLAF1	chr2:231335664-231338387	GM12878	blood:	n/a	chr2:231335975-231335984 chr2:231338274-231338283
2	ATF2	chr2:231336631-231337934	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:231336539-231336787	GM12878	blood:	n/a	n/a
4	GATA3	chr2:231336596-231336962	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:231335798-231337208	GM12891	blood:	n/a	n/a
6	POLR2A	chr2:231335276-231338471	GM12892	blood:	n/a	n/a
7	NFATC1	chr2:231335712-231336915	GM12878	blood:	n/a	n/a
8	PML	chr2:231335735-231338638	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:231335747-231338559	GM12892	blood:	n/a	n/a
10	POLR2A	chr2:231335449-231339009	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:231335649-231338240	K562	blood:	n/a	n/a
12	POLR2A	chr2:231335842-231337023	GM12878	blood:	n/a	n/a
13	MTA3	chr2:231335661-231338637	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:231335716-231337240	GM12891	blood:	n/a	n/a
15	POLR2A	chr2:231335737-231338557	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:231335286-231337246	GM12892	blood:	n/a	n/a
17	GATA3	chr2:231336522-231336971	SK-N-SH	brain:	n/a	chr2:231336532-231336539
18	NFIC	chr2:231335632-231336832	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:231335249-231338407	GM12892	blood:	n/a	n/a
20	POLR2A	chr2:231335774-231337204	GM12891	blood:	n/a	n/a
21	POLR2A	chr2:231335709-231338537	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:231335855-231338552	GM12891	blood:	n/a	n/a
23	RCOR1	chr2:231336678-231336993	K562	blood:	n/a	n/a
24	POLR2A	chr2:231336239-231336806	GM12891	blood:	n/a	n/a
25	JUND	chr2:231336662-231337046	K562	blood:	n/a	n/a

Variant related genes	Relation type
SP100	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1051579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1051580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1051581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1382699	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1479177	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1564323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1600297	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613630	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1649863	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1649864	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1649866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1649867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1649871	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1649872	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1649873	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1649874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1649875	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1649878	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1649882	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]
rs1649883	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]
rs1649886	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]
rs1649888	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1649889	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]
rs1649891	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]
rs1649928	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678162	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]
rs1678163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678164	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678165	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678167	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]
rs1678168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678169	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678200	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678201	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678204	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17274304	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17333468	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17333482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17333503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303609	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2306274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2306276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2434048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2559088	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2619158	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2619159	0.91[ASN][1000 genomes]
rs3769853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769854	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769856	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]
rs6436938	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6739283	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73000277	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7878	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]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1649887	SP100	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 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	chr2:231308800-231337000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:231308800-231337400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:231309600-231336800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:231312400-231337000	Weak transcription	HepG2	liver
7	chr2:231312400-231337200	Weak transcription	Hela-S3	cervix
8	chr2:231319800-231336800	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr2:231319800-231336800	Strong transcription	HSMM	muscle
10	chr2:231321800-231338600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:231322200-231340200	Strong transcription	Liver	Liver
12	chr2:231322600-231336800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:231322600-231336800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr2:231322600-231338200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:231322800-231336800	Strong transcription	Adipose Nuclei	Adipose
16	chr2:231322800-231336800	Strong transcription	Fetal Thymus	thymus
17	chr2:231323000-231336800	Strong transcription	Thymus	Thymus
18	chr2:231323400-231336800	Strong transcription	Primary T cells from cord blood	blood
19	chr2:231323400-231337600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:231323800-231337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:231324000-231336800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:231324400-231336800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:231325800-231336800	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:231325800-231338400	Strong transcription	Left Ventricle	heart
25	chr2:231325800-231338600	Strong transcription	Lung	lung
26	chr2:231325800-231338800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:231326000-231336800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:231326000-231336800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:231327000-231337000	Strong transcription	HUVEC	blood vessel
30	chr2:231328200-231338400	Strong transcription	Fetal Muscle Leg	muscle
31	chr2:231328400-231336800	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:231329600-231343800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:231330000-231337400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr2:231331200-231338400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr2:231331400-231336800	Strong transcription	Colon Smooth Muscle	Colon
36	chr2:231331400-231337000	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:231332000-231345200	Weak transcription	Brain Substantia Nigra	brain
38	chr2:231332200-231338200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:231332400-231344400	Weak transcription	Gastric	stomach
40	chr2:231332800-231339200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:231333400-231339800	Genic enhancers	Primary B cells from cord blood	blood
42	chr2:231334000-231336800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:231334000-231336800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr2:231334200-231336800	Strong transcription	Colonic Mucosa	Colon
45	chr2:231334200-231356000	Weak transcription	Fetal Intestine Small	intestine
46	chr2:231334600-231336800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:231334600-231340000	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr2:231334800-231337200	Weak transcription	NHEK	skin
49	chr2:231334800-231358400	Weak transcription	Fetal Stomach	stomach
50	chr2:231335000-231337400	Weak transcription	HMEC	breast

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