Variant report

Variant	rs2542589
Chromosome Location	chr2:54021225-54021226
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54013384..54018041-chr2:54019563..54022732,5	K562	blood:
2	chr2:54019955..54022961-chr2:54036087..54038626,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115239	Chromatin interaction
ENSG00000068912	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10490468	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11897282	0.92[CHB][hapmap];0.87[ASN][1000 genomes]
rs11901698	0.93[CHB][hapmap]
rs1232	0.92[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs13408029	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs17045176	0.93[CHB][hapmap];0.89[ASN][1000 genomes]
rs17045199	0.83[CEU][hapmap]
rs17045203	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs17520505	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs17521008	0.86[ASN][1000 genomes]
rs2287340	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs2302797	0.92[CHB][hapmap];0.87[ASN][1000 genomes]
rs2542572	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2542573	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542578	0.83[ASN][1000 genomes]
rs2542580	0.88[ASN][1000 genomes]
rs2542582	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2542583	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542590	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542591	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542592	0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2543629	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs2692512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692513	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692516	0.88[CEU][hapmap]
rs2692519	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692521	0.92[ASN][1000 genomes]
rs2692522	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2692523	0.83[ASN][1000 genomes]
rs2692530	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2692533	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2692534	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs2909262	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2949813	0.85[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2949814	0.86[ASN][1000 genomes]
rs35772199	0.86[ASN][1000 genomes]
rs3770394	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs3770395	0.87[ASN][1000 genomes]
rs3770397	0.89[ASN][1000 genomes]
rs3770399	0.87[ASN][1000 genomes]
rs3770411	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs4116709	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs55897904	0.80[ASN][1000 genomes]
rs58326257	0.80[ASN][1000 genomes]
rs62137573	0.86[ASN][1000 genomes]
rs62137602	0.89[ASN][1000 genomes]
rs62137606	0.87[ASN][1000 genomes]
rs62137610	0.83[ASN][1000 genomes]
rs62137611	0.83[ASN][1000 genomes]
rs62137612	0.83[ASN][1000 genomes]
rs6730006	0.87[ASN][1000 genomes]
rs719127	0.93[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs72901256	0.88[ASN][1000 genomes]
rs7600817	0.87[ASN][1000 genomes]
rs805316	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs805334	0.87[CEU][hapmap];0.91[CHB][hapmap]
rs805338	0.93[CHB][hapmap]
rs805368	0.87[ASN][1000 genomes]
rs805383	0.88[ASN][1000 genomes]
rs805385	0.88[ASN][1000 genomes]
rs805398	0.84[ASN][1000 genomes]
rs805435	0.88[ASN][1000 genomes]
rs805437	0.88[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805446	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs805447	0.93[CHB][hapmap]
rs805449	0.92[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	chr2:54015200-54024000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:54015200-54025400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:54015200-54029800	Weak transcription	Esophagus	oesophagus
4	chr2:54015200-54038200	Weak transcription	Small Intestine	intestine
5	chr2:54015200-54046200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:54015200-54046200	Weak transcription	Aorta	Aorta
7	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
8	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:54015400-54021600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:54015600-54021600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:54015600-54022000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:54015600-54022200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:54015600-54022200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:54015600-54022200	Weak transcription	Brain Germinal Matrix	brain
15	chr2:54015600-54022200	Weak transcription	Fetal Kidney	kidney
16	chr2:54015600-54022800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:54015600-54029600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:54015600-54035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:54015600-54035800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:54015800-54021400	Weak transcription	Fetal Thymus	thymus
22	chr2:54015800-54021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:54015800-54022000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:54015800-54022000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:54015800-54022000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:54015800-54022000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:54015800-54022000	Weak transcription	Adipose Nuclei	Adipose
28	chr2:54015800-54022000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:54015800-54022000	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:54015800-54022000	Weak transcription	NH-A	brain
31	chr2:54015800-54022200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:54015800-54022200	Weak transcription	Primary T cells from cord blood	blood
33	chr2:54015800-54022200	Weak transcription	Fetal Intestine Large	intestine
34	chr2:54015800-54022200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:54015800-54022200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:54015800-54022200	Weak transcription	Thymus	Thymus
37	chr2:54015800-54022200	Weak transcription	K562	blood
38	chr2:54015800-54022200	Weak transcription	NHEK	skin
39	chr2:54015800-54022400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:54015800-54022400	Weak transcription	Primary B cells from cord blood	blood
41	chr2:54015800-54022600	Weak transcription	Brain Anterior Caudate	brain
42	chr2:54015800-54022800	Weak transcription	Fetal Brain Female	brain
43	chr2:54015800-54023600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:54015800-54023600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:54015800-54023600	Weak transcription	HSMMtube	muscle
46	chr2:54015800-54024400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:54015800-54024800	Weak transcription	HUVEC	blood vessel
48	chr2:54015800-54025000	Weak transcription	Right Ventricle	heart
49	chr2:54015800-54025200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:54015800-54026000	Weak transcription	Fetal Brain Male	brain

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