Variant report

Variant	rs13116341
Chromosome Location	chr4:26840684-26840685
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	chr4:26834747..26837079-chr4:26840083..26841979,2	MCF-7	breast:
2	chr4:26840051..26842840-chr4:26845886..26847935,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10029307	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11729927	0.81[ASN][1000 genomes]
rs11730235	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11737218	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11943948	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12641261	0.88[ASN][1000 genomes]
rs12644073	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12646473	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12650172	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs13138942	0.83[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13139464	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28497454	0.81[ASN][1000 genomes]
rs34996346	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3792685	0.90[JPT][hapmap]
rs3924178	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4274829	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4407490	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4505809	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4519790	0.96[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4532223	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4557250	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4557251	0.91[ASN][1000 genomes]
rs57663175	0.80[ASN][1000 genomes]
rs57686546	0.80[ASN][1000 genomes]
rs58075729	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58968032	0.86[ASN][1000 genomes]
rs6448479	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6448484	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6448488	0.95[JPT][hapmap]
rs6815719	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6833053	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6833895	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6835631	0.95[JPT][hapmap]
rs6844153	0.95[JPT][hapmap]
rs6853032	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73811400	0.87[ASN][1000 genomes]
rs73813220	0.82[ASN][1000 genomes]
rs7655686	0.82[ASN][1000 genomes]
rs9790789	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][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	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1001306	chr4:26821511-26955344	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13116341	RP11-293A21.1	cis	Thyroid	GTEx
rs13116341	RP11-293A21.1	cis	Adipose Subcutaneous	GTEx
rs13116341	RP11-293A21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs13116341	STIM2	cis	multi-tissue	Pritchard
rs13116341	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs13116341	RP11-293A21.1	cis	lung	GTEx
rs13116341	RP11-293A21.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26830000-26841200	Weak transcription	Small Intestine	intestine
2	chr4:26831600-26841200	Weak transcription	Ovary	ovary
3	chr4:26838200-26841200	Weak transcription	Right Atrium	heart
4	chr4:26838400-26841200	Weak transcription	Lung	lung
5	chr4:26839200-26843200	Enhancers	Fetal Heart	heart
6	chr4:26839600-26841800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr4:26839600-26842400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:26839600-26842400	Enhancers	Fetal Muscle Leg	muscle
9	chr4:26839800-26841000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:26840000-26840800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr4:26840000-26841000	Weak transcription	Fetal Stomach	stomach
12	chr4:26840000-26841000	Weak transcription	Left Ventricle	heart
13	chr4:26840000-26841000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:26840000-26841200	Weak transcription	Adipose Nuclei	Adipose
15	chr4:26840000-26841400	Enhancers	Fetal Intestine Large	intestine
16	chr4:26840000-26841400	Enhancers	Fetal Intestine Small	intestine
17	chr4:26840000-26841400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:26840000-26841600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr4:26840000-26842200	Weak transcription	Fetal Thymus	thymus
20	chr4:26840000-26842400	Enhancers	Fetal Lung	lung
21	chr4:26840000-26858800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:26840200-26840800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:26840200-26840800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:26840200-26840800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr4:26840200-26841200	Weak transcription	Thymus	Thymus
26	chr4:26840400-26841400	Enhancers	Duodenum Mucosa	Duodenum
27	chr4:26840400-26841600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr4:26840400-26841600	Enhancers	Osteobl	bone
29	chr4:26840600-26841000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:26840600-26841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:26840600-26841600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:26840600-26844200	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links