Variant report

Variant	rs35274
Chromosome Location	chr5:58645805-58645806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58645161..58647091-chr5:58651070..58653977,2	K562	blood:

Variant related genes	Relation type
ENSG00000113448	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs154031	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs168641	0.87[ASN][1000 genomes]
rs2441091	0.81[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs244573	0.90[AFR][1000 genomes]
rs244574	0.96[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs244575	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs244577	0.95[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs244579	1.00[YRI][hapmap]
rs244582	0.87[ASN][1000 genomes]
rs244583	0.87[ASN][1000 genomes]
rs244586	0.83[ASN][1000 genomes]
rs244587	0.83[CHD][hapmap]
rs244588	0.81[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs35258	0.82[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs35263	0.89[EUR][1000 genomes]
rs35267	0.89[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35276	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35277	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35278	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35279	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35283	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs35284	0.89[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs39672	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs40122	0.89[ASW][hapmap]
rs40126	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40328	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1022160	chr5:58645805-58689010	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35274	RAB3C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58634400-58647800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:58635200-58652600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:58637200-58646000	Weak transcription	Psoas Muscle	Psoas
4	chr5:58640200-58646000	Weak transcription	Right Ventricle	heart
5	chr5:58641200-58648000	Enhancers	A549	lung
6	chr5:58641800-58646600	Weak transcription	Fetal Brain Female	brain
7	chr5:58642200-58653200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:58642600-58646800	Weak transcription	Brain Angular Gyrus	brain
9	chr5:58642600-58647000	Weak transcription	Fetal Stomach	stomach
10	chr5:58642600-58652600	Weak transcription	Fetal Brain Male	brain
11	chr5:58642600-58652600	Weak transcription	Small Intestine	intestine
12	chr5:58643200-58646600	Weak transcription	Brain Substantia Nigra	brain
13	chr5:58643200-58646600	Weak transcription	Fetal Lung	lung
14	chr5:58643200-58647000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:58643200-58647000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:58643600-58652400	Weak transcription	Fetal Kidney	kidney
17	chr5:58643800-58646000	Weak transcription	Brain Hippocampus Middle	brain
18	chr5:58643800-58646000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:58644200-58650400	Enhancers	Fetal Heart	heart
20	chr5:58644400-58646600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:58644800-58648600	Weak transcription	Hela-S3	cervix
22	chr5:58645000-58646000	Weak transcription	Left Ventricle	heart
23	chr5:58645000-58646600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr5:58645800-58646000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr5:58645800-58647600	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links