Variant report

Variant	rs6495273
Chromosome Location	chr15:78413275-78413276
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	chr15:78411897..78414828-chr15:78414892..78418172,3	MCF-7	breast:
2	chr15:78413156..78413707-chr15:78471986..78472640,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10456	0.90[CEU][hapmap]
rs11072727	0.87[ASN][1000 genomes]
rs11072728	0.81[CEU][hapmap];0.87[ASN][1000 genomes]
rs11072729	0.81[CEU][hapmap];0.85[ASN][1000 genomes]
rs12440984	0.91[CEU][hapmap]
rs1542100	0.82[ASN][1000 genomes]
rs16969514	0.86[ASN][1000 genomes]
rs1971151	0.85[ASN][1000 genomes]
rs2304829	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784328	0.81[ASN][1000 genomes]
rs3784330	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs59999498	0.87[ASN][1000 genomes]
rs62009270	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62009271	0.87[ASN][1000 genomes]
rs7161765	0.86[ASN][1000 genomes]
rs7162025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164338	0.81[CEU][hapmap];0.88[ASN][1000 genomes]
rs7359294	0.81[ASN][1000 genomes]
rs8028859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8032449	0.91[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8036417	0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9806257	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6495273	CIB2	cis	Esophagus Mucosa	GTEx
rs6495273	CIB2	cis	multi-tissue	Pritchard
rs6495273	CIB2	cis	Muscle Skeletal	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78396200-78421800	Weak transcription	Right Ventricle	heart
2	chr15:78396600-78423800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:78397600-78421400	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:78398400-78423200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:78400000-78422400	Weak transcription	Brain Germinal Matrix	brain
6	chr15:78400200-78414600	Weak transcription	Fetal Brain Female	brain
7	chr15:78401400-78414400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:78405600-78421400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:78406000-78414200	Weak transcription	Fetal Intestine Large	intestine
10	chr15:78406000-78421600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:78406000-78423000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:78406400-78420000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:78406400-78423000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr15:78409000-78423000	Weak transcription	Brain Anterior Caudate	brain
15	chr15:78412200-78417200	Strong transcription	Thymus	Thymus
16	chr15:78412200-78419200	Strong transcription	Fetal Intestine Small	intestine
17	chr15:78412400-78413800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr15:78412600-78413600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr15:78412600-78413600	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr15:78412600-78413800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr15:78412800-78413400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr15:78412800-78413600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr15:78412800-78413600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr15:78412800-78413600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:78412800-78413600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:78412800-78413800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr15:78412800-78413800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr15:78412800-78413800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr15:78412800-78413800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:78412800-78416000	Strong transcription	Fetal Thymus	thymus
31	chr15:78413000-78413400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:78413000-78413600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr15:78413000-78413600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:78413000-78413800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:78413000-78417800	Strong transcription	Fetal Stomach	stomach
36	chr15:78413200-78413600	Enhancers	Right Atrium	heart
37	chr15:78413200-78413600	Active TSS	Spleen	Spleen
38	chr15:78413200-78413800	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links