Variant report

Variant	rs2287340
Chromosome Location	chr2:53992859-53992860
allele	G/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	MYC	chr2:53992655-53993520	K562	blood:	n/a	chr2:53993471-53993480 chr2:53992674-53992684
2	GATA1	chr2:53992640-53993785	PBDE	blood:	n/a	n/a
3	ZNF263	chr2:53992769-53993453	HEK293-T-REx	kidney:	n/a	n/a

Variant related genes	Relation type
GPR75-ASB3	TF binding region
CHAC2	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10490468	0.92[CHB][hapmap];0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs11897282	1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[ASN][1000 genomes]
rs11901698	1.00[CHB][hapmap]
rs1232	0.84[CHB][hapmap]
rs13408029	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs17045176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17045203	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17520505	0.92[CHB][hapmap]
rs17520854	0.83[AMR][1000 genomes]
rs17521008	0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs2302797	1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[ASN][1000 genomes]
rs2542572	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2542573	0.83[ASN][1000 genomes]
rs2542580	0.82[ASN][1000 genomes]
rs2542581	0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs2542582	0.92[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2542583	0.88[ASN][1000 genomes]
rs2542589	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs2542590	0.84[ASN][1000 genomes]
rs2542591	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs2542592	0.84[CHB][hapmap]
rs2543629	0.92[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs2692512	0.80[ASN][1000 genomes]
rs2692513	0.80[ASN][1000 genomes]
rs2692519	0.92[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs2692522	0.83[ASN][1000 genomes]
rs2692530	0.90[ASN][1000 genomes]
rs2692533	0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs2692535	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2909262	0.89[ASN][1000 genomes]
rs2949813	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3770394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3770395	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3770397	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3770399	0.84[ASN][1000 genomes]
rs3770411	0.92[CHB][hapmap];0.82[CHD][hapmap]
rs3922262	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4116709	0.92[CHB][hapmap]
rs55897904	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58326257	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62137573	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62137602	0.87[ASN][1000 genomes]
rs62137606	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62137610	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62137611	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62137612	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6730006	0.84[ASN][1000 genomes]
rs719127	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs72901256	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7600817	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs805316	0.84[CHB][hapmap]
rs805334	0.81[CHB][hapmap]
rs805338	0.84[CHB][hapmap]
rs805435	0.82[ASN][1000 genomes]
rs805437	0.84[CHB][hapmap]
rs805446	0.84[CHB][hapmap]
rs805447	0.84[CHB][hapmap]
rs805449	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
3	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:53958200-53994400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:53963000-53994000	Weak transcription	A549	lung
8	chr2:53973400-53994400	Weak transcription	Colonic Mucosa	Colon
9	chr2:53975800-53994400	Weak transcription	Fetal Kidney	kidney
10	chr2:53978800-53994200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:53979400-53994000	Weak transcription	Osteobl	bone
12	chr2:53979800-53994200	Weak transcription	Psoas Muscle	Psoas
13	chr2:53979800-53994200	Weak transcription	NHLF	lung
14	chr2:53982400-53994400	Weak transcription	NHDF-Ad	bronchial
15	chr2:53982800-53994000	Weak transcription	HMEC	breast
16	chr2:53982800-53994200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:53983000-53994000	Weak transcription	Small Intestine	intestine
18	chr2:53983200-53993200	Strong transcription	Primary T cells from cord blood	blood
19	chr2:53984200-53993000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:53984200-53994200	Weak transcription	HSMMtube	muscle
21	chr2:53984200-53994400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:53984200-53994400	Weak transcription	Lung	lung
23	chr2:53984200-53994400	Weak transcription	Right Ventricle	heart
24	chr2:53984600-53994400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:53984800-53994200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:53984800-53994400	Weak transcription	Brain Angular Gyrus	brain
27	chr2:53986400-53994000	Weak transcription	Brain Germinal Matrix	brain
28	chr2:53986400-53994000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:53986400-53994600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:53987200-53994400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:53988600-53993000	Strong transcription	Fetal Thymus	thymus
32	chr2:53989000-53993000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:53989000-53993200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:53989800-53994200	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:53990600-53993400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:53990600-53993800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:53990800-53993400	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:53990800-53993400	Weak transcription	Thymus	Thymus
39	chr2:53990800-53994000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:53990800-53994000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:53990800-53994000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:53990800-53994000	Weak transcription	HUVEC	blood vessel
43	chr2:53990800-53994000	Weak transcription	NHEK	skin
44	chr2:53990800-53994200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:53990800-53994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:53990800-53994200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:53990800-53994200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:53990800-53994200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:53990800-53994200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:53990800-53994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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