Variant report

Variant	rs6858964
Chromosome Location	chr5:58861037-58861038
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	chr5:58843792..58846510-chr5:58858792..58861752,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10059809	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10065078	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1395335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1395336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1395337	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs294494	0.95[MEX][hapmap]
rs294496	0.95[MEX][hapmap]
rs294497	0.95[MEX][hapmap]
rs294498	0.82[ASW][hapmap];0.95[MEX][hapmap]
rs294501	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs296406	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs37579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40215	0.88[ASW][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs6890180	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs697076	0.94[ASW][hapmap];0.88[CHB][hapmap]
rs702544	0.88[CHB][hapmap];0.83[JPT][hapmap]

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	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv462189	chr5:58830145-58879822	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598255	chr5:58830145-58879822	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6858964	FLJ37543	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58843800-58862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:58854600-58861600	Weak transcription	Fetal Brain Female	brain
3	chr5:58855600-58863000	Enhancers	Primary B cells from peripheral blood	blood
4	chr5:58856600-58864000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:58856600-58865400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:58858600-58861400	Enhancers	Stomach Mucosa	stomach
7	chr5:58858600-58862600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr5:58858800-58861600	Enhancers	Thymus	Thymus
9	chr5:58859200-58861200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:58859200-58883400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:58859400-58865200	Weak transcription	Brain Substantia Nigra	brain
12	chr5:58859400-58870400	Weak transcription	Fetal Intestine Large	intestine
13	chr5:58859400-58871600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:58859400-58884000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:58859600-58862600	Enhancers	Hela-S3	cervix
16	chr5:58859600-58864800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:58859800-58861800	Enhancers	Psoas Muscle	Psoas
18	chr5:58859800-58863200	Weak transcription	Fetal Lung	lung
19	chr5:58859800-58864400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:58859800-58865400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:58859800-58873800	Weak transcription	HSMM	muscle
22	chr5:58860000-58866200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:58860200-58861400	Weak transcription	GM12878-XiMat	blood
24	chr5:58860200-58861600	Weak transcription	HUVEC	blood vessel
25	chr5:58860200-58863600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:58860200-58864000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:58860200-58873600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr5:58860400-58861800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr5:58860400-58862600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:58860400-58865600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr5:58860600-58861600	Enhancers	Gastric	stomach
32	chr5:58860600-58861800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:58860600-58861800	Transcr. at gene 5' and 3'	A549	lung
34	chr5:58860800-58861200	Enhancers	Fetal Intestine Small	intestine
35	chr5:58860800-58861600	Enhancers	Lung	lung
36	chr5:58860800-58862600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:58860800-58865000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:58861000-58861400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:58861000-58861800	Enhancers	Primary B cells from cord blood	blood
40	chr5:58861000-58870400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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