Variant report

Variant	rs8027371
Chromosome Location	chr15:43417663-43417664
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	chr15:43397628..43400398-chr15:43414771..43418048,4	MCF-7	breast:
2	chr15:43415478..43417953-chr15:43419432..43421358,2	K562	blood:

Variant related genes	Relation type
ENSG00000159459	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11070386	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs11070391	0.80[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11070396	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[ASN][1000 genomes]
rs11630595	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs11855754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12592725	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12899266	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1462856	0.80[CEU][hapmap]
rs16957511	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1834643	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2037392	1.00[CEU][hapmap]
rs2042742	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2241516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2412751	0.81[YRI][hapmap]
rs2412752	0.81[JPT][hapmap]
rs28585036	1.00[ASW][hapmap];0.86[CEU][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap]
rs2899077	0.86[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap]
rs2947019	0.92[ASW][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap]
rs34646108	0.89[ASN][1000 genomes]
rs3736054	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs3784267	0.89[ASN][1000 genomes]
rs3784268	0.82[ASN][1000 genomes]
rs3803341	0.80[CEU][hapmap]
rs4573908	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs4923955	0.80[CEU][hapmap]
rs4924704	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs4924709	0.87[ASN][1000 genomes]
rs494863	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs495286	0.92[ASW][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap]
rs497138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs499280	0.93[ASN][1000 genomes]
rs530305	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[ASN][1000 genomes]
rs531850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs538218	0.83[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap]
rs540587	0.94[JPT][hapmap]
rs6493076	0.80[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6493077	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs6493078	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174915	0.80[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7176116	0.80[ASN][1000 genomes]
rs7178567	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs7183814	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs8027733	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs8036710	0.80[ASN][1000 genomes]
rs8037022	0.80[CEU][hapmap]
rs8042481	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	esv1802035	chr15:43370916-43487742	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8027371	TTBK2	cis	parietal	SCAN
rs8027371	TGM5	cis	lymphoblastoid	seeQTL
rs8027371	ELL3	cis	lymphoblastoid	seeQTL
rs8027371	C15orf63	cis	lymphoblastoid	seeQTL
rs8027371	MGST3	trans	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43415400-43419200	Weak transcription	Small Intestine	intestine
2	chr15:43415600-43419200	Weak transcription	Pancreas	Pancrea
3	chr15:43415600-43419600	Weak transcription	Stomach Mucosa	stomach
4	chr15:43415600-43425200	Weak transcription	Gastric	stomach
5	chr15:43415800-43417800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr15:43415800-43418200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr15:43415800-43418200	Weak transcription	Colonic Mucosa	Colon
8	chr15:43415800-43419400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:43415800-43419800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:43415800-43419800	Weak transcription	Liver	Liver
11	chr15:43415800-43425000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:43415800-43425000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:43415800-43425000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:43415800-43425000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:43415800-43425000	Weak transcription	Aorta	Aorta
16	chr15:43415800-43425000	Weak transcription	Brain Anterior Caudate	brain
17	chr15:43415800-43425200	Weak transcription	Esophagus	oesophagus
18	chr15:43416200-43418000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:43416200-43419800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:43416200-43419800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:43416200-43419800	Weak transcription	A549	lung
22	chr15:43416200-43425000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr15:43416800-43419800	Enhancers	Fetal Intestine Large	intestine
24	chr15:43417000-43420600	Enhancers	Fetal Intestine Small	intestine
25	chr15:43417400-43419600	Enhancers	Duodenum Mucosa	Duodenum
26	chr15:43417600-43418000	Flanking Active TSS	HepG2	liver
27	chr15:43417600-43419800	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr15:43417600-43425000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:43417600-43425000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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