Variant report

Variant	rs39672
Chromosome Location	chr5:58643075-58643076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58623297..58625750-chr5:58642406..58644812,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs154024	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs154031	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs168641	0.93[ASN][1000 genomes]
rs2441091	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs244573	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs244574	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs244577	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs244579	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs244582	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs244583	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs244586	0.88[ASN][1000 genomes]
rs244588	0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs35258	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35261	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs35267	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35274	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35277	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35279	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35283	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35284	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40122	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs40126	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs40328	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs434274	0.82[YRI][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	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1032732	chr5:58637179-58689010	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58625000-58644600	Weak transcription	Left Ventricle	heart
2	chr5:58634400-58647800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:58635200-58652600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:58637200-58646000	Weak transcription	Psoas Muscle	Psoas
5	chr5:58640200-58646000	Weak transcription	Right Ventricle	heart
6	chr5:58641200-58648000	Enhancers	A549	lung
7	chr5:58641400-58643200	Enhancers	Colon Smooth Muscle	Colon
8	chr5:58641600-58643200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr5:58641600-58643800	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr5:58641800-58643200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr5:58641800-58646600	Weak transcription	Fetal Brain Female	brain
12	chr5:58642200-58643200	Enhancers	Brain Substantia Nigra	brain
13	chr5:58642200-58644400	Enhancers	Rectal Smooth Muscle	rectum
14	chr5:58642200-58653200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:58642600-58643600	Enhancers	Fetal Kidney	kidney
16	chr5:58642600-58646800	Weak transcription	Brain Angular Gyrus	brain
17	chr5:58642600-58647000	Weak transcription	Fetal Stomach	stomach
18	chr5:58642600-58652600	Weak transcription	Fetal Brain Male	brain
19	chr5:58642600-58652600	Weak transcription	Small Intestine	intestine
20	chr5:58642800-58643200	Enhancers	Brain Hippocampus Middle	brain
21	chr5:58642800-58643200	Enhancers	Fetal Lung	lung
22	chr5:58642800-58644200	Weak transcription	Fetal Heart	heart
23	chr5:58642800-58644200	Weak transcription	Hela-S3	cervix
24	chr5:58643000-58643200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:58643000-58643200	Enhancers	Brain Cingulate Gyrus	brain

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