Variant report

Variant	rs12203248
Chromosome Location	chr6:5090973-5090974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:5080171..5082939-chr6:5089292..5092079,2	MCF-7	breast:
2	chr6:5083037..5085353-chr6:5088863..5093171,5	MCF-7	breast:
3	chr6:5087646..5089751-chr6:5090189..5093057,2	K562	blood:
4	chr6:5079785..5081381-chr6:5089374..5091355,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10458182	1.00[ASN][1000 genomes]
rs10484846	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242990	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242991	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242993	0.82[EUR][1000 genomes]
rs12110634	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111219	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191255	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192552	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12192863	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193229	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195956	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202160	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202384	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204382	1.00[ASN][1000 genomes]
rs12204490	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206931	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17139439	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35400671	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425930	0.88[EUR][1000 genomes]
rs434350	1.00[ASN][1000 genomes]
rs460111	0.88[EUR][1000 genomes]
rs467373	0.88[EUR][1000 genomes]
rs4959330	1.00[ASN][1000 genomes]
rs4959331	1.00[ASN][1000 genomes]
rs4960066	0.84[EUR][1000 genomes]
rs4960068	1.00[ASN][1000 genomes]
rs6597114	1.00[ASN][1000 genomes]
rs6597115	1.00[ASN][1000 genomes]
rs6911123	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811642	1.00[ASN][1000 genomes]
rs72811643	1.00[ASN][1000 genomes]
rs761365	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757651	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405800	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405801	0.84[EUR][1000 genomes]
rs9504354	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1017373	chr6:5066785-5128943	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv538112	chr6:5066785-5128943	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
10	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12203248	RP11-428J1.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5089600-5091000	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr6:5089800-5091000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:5090000-5092600	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:5090200-5091000	Enhancers	Right Atrium	heart
5	chr6:5090200-5091200	Enhancers	Left Ventricle	heart
6	chr6:5090200-5091400	Enhancers	Fetal Heart	heart
7	chr6:5090400-5091000	Enhancers	Right Ventricle	heart
8	chr6:5090400-5091000	Enhancers	Spleen	Spleen
9	chr6:5090400-5091400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:5090400-5091400	Bivalent Enhancer	Fetal Thymus	thymus
11	chr6:5090400-5091600	Enhancers	Fetal Muscle Leg	muscle
12	chr6:5090400-5092400	Flanking Active TSS	GM12878-XiMat	blood
13	chr6:5090600-5091000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:5090600-5091000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:5090600-5091000	Strong transcription	Aorta	Aorta
16	chr6:5090600-5091000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr6:5090600-5091000	Bivalent Enhancer	Lung	lung
18	chr6:5090600-5091000	Enhancers	Pancreas	Pancrea
19	chr6:5090600-5091600	Enhancers	Adipose Nuclei	Adipose
20	chr6:5090600-5093600	Weak transcription	Brain Anterior Caudate	brain
21	chr6:5090600-5095600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:5090800-5091000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
23	chr6:5090800-5091000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
24	chr6:5090800-5091000	Enhancers	Esophagus	oesophagus
25	chr6:5090800-5091200	Enhancers	Placenta	Placenta
26	chr6:5090800-5091600	Enhancers	Primary T cells from cord blood	blood
27	chr6:5090800-5091600	Genic enhancers	HepG2	liver
28	chr6:5090800-5093600	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links