Variant report

Variant	rs17343071
Chromosome Location	chr15:74805451-74805452
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	chr15:74802902..74805887-chr15:74821101..74823845,2	MCF-7	breast:
2	chr15:74802902..74806494-chr15:74809022..74812313,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARID3B-1	chr15:74804733-74806312	XLOC_011313

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11629492	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11632086	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11633697	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11634261	1.00[AMR][1000 genomes]
rs11637129	0.98[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs16970078	0.82[ASW][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap]
rs16970170	0.82[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28362914	0.81[AFR][1000 genomes]
rs55936349	0.90[AFR][1000 genomes]
rs56253831	0.92[AFR][1000 genomes]
rs57317343	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57592570	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60130631	1.00[AMR][1000 genomes]
rs74025808	0.90[AFR][1000 genomes]
rs74025809	0.88[AFR][1000 genomes]
rs74025810	0.92[AFR][1000 genomes]
rs74025811	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs74025821	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1809847	chr15:74734500-74948063	Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1044797	chr15:74773661-74819852	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17343071	SCAMP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74762600-74807400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr15:74774000-74815200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:74775800-74807000	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:74782400-74811400	Weak transcription	Stomach Mucosa	stomach
5	chr15:74782800-74806000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:74782800-74807400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:74795200-74806600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:74797600-74808200	Weak transcription	Fetal Stomach	stomach
9	chr15:74798600-74815600	Weak transcription	Thymus	Thymus
10	chr15:74798800-74807600	Weak transcription	Primary T cells from cord blood	blood
11	chr15:74798800-74809200	Weak transcription	HMEC	breast
12	chr15:74799000-74806200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:74799000-74809200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:74799000-74809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:74799000-74811400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr15:74803200-74805800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr15:74803400-74811800	Weak transcription	HSMM	muscle
18	chr15:74804800-74807200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:74804800-74809600	Weak transcription	Spleen	Spleen
20	chr15:74804800-74821000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:74805000-74805800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr15:74805000-74805800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr15:74805000-74805800	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr15:74805000-74807400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links