Variant report

Variant	rs12547493
Chromosome Location	chr8:8661534-8661535
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	chr8:8655376..8657753-chr8:8661368..8663526,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1039915	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1039916	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11249891	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11249893	0.86[EUR][1000 genomes]
rs11775523	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11777085	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11783966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11784052	0.85[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12544992	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12545499	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12677543	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12682352	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13254903	0.83[JPT][hapmap]
rs13259070	0.81[EUR][1000 genomes]
rs13259216	0.92[CEU][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13260419	0.88[ASN][1000 genomes]
rs13265731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1473029	0.90[ASN][1000 genomes]
rs1533058	0.85[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1533059	0.85[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1703982	0.81[AMR][1000 genomes]
rs2048419	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2271342	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2409091	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2409092	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2409096	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2428	0.85[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28399241	0.96[ASN][1000 genomes]
rs332039	0.83[JPT][hapmap]
rs332040	0.85[CEU][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap]
rs35039922	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35431455	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs408459	0.89[MEX][hapmap]
rs4382480	0.81[CEU][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap]
rs4481596	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4840362	0.85[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4841040	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4841042	0.85[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4841044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4841045	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4841051	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4841055	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs486781	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs560544	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57312668	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59046059	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60315134	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs609958	0.82[AMR][1000 genomes]
rs6601265	0.83[JPT][hapmap]
rs693109	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6988939	0.89[ASN][1000 genomes]
rs6993494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6994038	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7006589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7823757	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7832968	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs882462	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs907183	0.89[CEU][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap]
rs9644776	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1022511	chr8:8493992-8737132	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv539457	chr8:8493992-8737132	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	esv1824870	chr8:8583943-8699382	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv610189	chr8:8590437-8664940	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv831228	chr8:8608387-8790790	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv1018828	chr8:8609880-8790660	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv1022331	chr8:8610035-8787981	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12547493	RP11-62H7.2	cis	Thyroid	GTEx
rs12547493	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs12547493	ERI1	cis	brain	BrainEAC
rs12547493	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs12547493	ERI1	cis	cerebellar cortex	BrainEAC
rs12547493	SGK223	cis	Thyroid	GTEx
rs12547493	ERI1	cis	inferior olivary nucleus	BrainEAC
rs12547493	C8orf13	cis	multi-tissue	Pritchard
rs12547493	CLDN23	cis	multi-tissue	Pritchard
rs12547493	FAM86B3P	cis	Esophagus Mucosa	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8637600-8679800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:8649200-8666400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:8649400-8661800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr8:8649400-8663600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:8649400-8663800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr8:8650800-8663400	Weak transcription	Hela-S3	cervix
7	chr8:8653800-8662000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:8653800-8662600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr8:8653800-8663400	Weak transcription	HMEC	breast
10	chr8:8653800-8674800	Weak transcription	Brain Germinal Matrix	brain
11	chr8:8654000-8663600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr8:8654000-8666800	Weak transcription	NHDF-Ad	bronchial
13	chr8:8654000-8666800	Weak transcription	NHLF	lung
14	chr8:8654000-8671000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr8:8655000-8663400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr8:8655200-8662200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr8:8655200-8663400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr8:8655200-8663600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr8:8655200-8663800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr8:8655200-8666400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr8:8655200-8680600	Weak transcription	Colonic Mucosa	Colon
22	chr8:8655400-8662000	Weak transcription	Small Intestine	intestine
23	chr8:8655400-8662000	Weak transcription	Spleen	Spleen
24	chr8:8655400-8663600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr8:8655400-8663600	Weak transcription	HSMM	muscle
26	chr8:8655400-8666800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr8:8655600-8661600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr8:8655600-8673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr8:8655600-8685600	Weak transcription	Fetal Brain Female	brain
30	chr8:8655800-8661600	Weak transcription	Primary T cells from cord blood	blood
31	chr8:8655800-8662000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr8:8655800-8663600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr8:8655800-8666200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr8:8655800-8666800	Weak transcription	Fetal Brain Male	brain
35	chr8:8655800-8669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr8:8655800-8669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr8:8655800-8669200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr8:8655800-8669200	Weak transcription	Thymus	Thymus
39	chr8:8656000-8662000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr8:8656000-8662000	Weak transcription	Brain Angular Gyrus	brain
41	chr8:8656000-8663000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr8:8656000-8663600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr8:8656000-8669600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr8:8656200-8663600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr8:8656200-8667000	Weak transcription	Placenta	Placenta
46	chr8:8656200-8669000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr8:8656200-8669000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr8:8656400-8663600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr8:8656400-8663800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr8:8657400-8662800	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