Variant report

Variant	rs2973588
Chromosome Location	chr5:126125209-126125210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:126112394..126114255-chr5:126124910..126128811,3	MCF-7	breast:
2	chr5:126116007..126118146-chr5:126123068..126125342,2	K562	blood:
3	chr5:126121325..126123278-chr5:126123721..126126888,3	K562	blood:

Variant related genes	Relation type
ENSG00000113368	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10065951	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10478753	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1912570	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2136878	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2941661	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2941664	0.91[JPT][hapmap]
rs2941666	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2941673	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2973583	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2973587	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973589	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2973596	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2973600	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2973604	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2973886	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2973887	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2973890	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075655	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4267910	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62391702	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv949054	chr5:125918148-126254480	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv916675	chr5:126122436-126133000	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
4	nsv533306	chr5:126122436-126137162	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126114600-126141600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:126114600-126142000	Weak transcription	Spleen	Spleen
3	chr5:126114600-126161600	Weak transcription	Ovary	ovary
4	chr5:126115000-126140400	Weak transcription	Fetal Intestine Large	intestine
5	chr5:126115800-126131800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:126115800-126137400	Weak transcription	HSMM	muscle
7	chr5:126115800-126145800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:126116000-126141600	Weak transcription	Fetal Stomach	stomach
9	chr5:126116400-126128600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:126116400-126128600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr5:126116400-126128800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:126116400-126128800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:126116400-126130000	Weak transcription	Fetal Lung	lung
14	chr5:126116400-126137000	Weak transcription	Primary T cells from cord blood	blood
15	chr5:126116400-126140000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:126116400-126140200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:126116400-126140200	Weak transcription	Thymus	Thymus
18	chr5:126116400-126141000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:126116400-126143400	Weak transcription	Primary B cells from cord blood	blood
20	chr5:126116600-126131400	Weak transcription	Fetal Intestine Small	intestine
21	chr5:126116600-126140000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:126116600-126147800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:126116800-126128000	Weak transcription	HUVEC	blood vessel
24	chr5:126116800-126128600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:126117000-126135000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:126117000-126140800	Weak transcription	Fetal Brain Female	brain
27	chr5:126117800-126128400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr5:126117800-126128800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:126117800-126141200	Weak transcription	Brain Germinal Matrix	brain
30	chr5:126118000-126128800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr5:126118000-126137200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:126121000-126132400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:126121400-126125400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:126121400-126126600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:126121400-126128800	Strong transcription	Fetal Thymus	thymus
36	chr5:126121600-126125800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:126122200-126125800	Enhancers	HepG2	liver
38	chr5:126122600-126141000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr5:126123000-126132000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:126123000-126132000	Weak transcription	Hela-S3	cervix
41	chr5:126123600-126125400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:126123800-126125400	Enhancers	A549	lung
43	chr5:126123800-126125400	Enhancers	NHDF-Ad	bronchial
44	chr5:126124000-126126400	Enhancers	GM12878-XiMat	blood
45	chr5:126124000-126133200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:126124000-126140200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr5:126124200-126140200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr5:126124400-126127400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr5:126124400-126127800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr5:126124400-126128600	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links