Variant report

Variant	rs888127
Chromosome Location	chr12:11652829-11652830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1005265	0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10743960	0.91[YRI][hapmap];0.93[AFR][1000 genomes]
rs10772478	1.00[ASW][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1212288	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs17209646	0.89[CHD][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1974695	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2900174	0.83[ASW][hapmap]
rs2908831	0.95[AFR][1000 genomes]
rs2908836	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2908838	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2951770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2951775	0.87[YRI][hapmap]
rs2951783	0.92[ASW][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.91[YRI][hapmap]
rs2965703	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4237932	0.92[ASW][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs7342388	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs888125	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs963878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription 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	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv557572	chr12:11575570-11693121	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv469112	chr12:11575570-11711690	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv557573	chr12:11575570-11711690	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv976577	chr12:11651148-11653761	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11651800-11653200	Weak transcription	GM12878-XiMat	blood
2	chr12:11652000-11653600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr12:11652200-11655000	Active TSS	Brain Angular Gyrus	brain
4	chr12:11652600-11653000	Active TSS	Brain Anterior Caudate	brain
5	chr12:11652600-11653000	Active TSS	Brain Hippocampus Middle	brain
6	chr12:11652600-11655200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:11652800-11653000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr12:11652800-11653000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
9	chr12:11652800-11653000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr12:11652800-11653000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
11	chr12:11652800-11653000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:11652800-11653000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:11652800-11653000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:11652800-11653000	Active TSS	Brain Cingulate Gyrus	brain
15	chr12:11652800-11653000	Active TSS	Brain Germinal Matrix	brain
16	chr12:11652800-11653000	Bivalent Enhancer	Brain Substantia Nigra	brain
17	chr12:11652800-11653000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
18	chr12:11652800-11653200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr12:11652800-11653200	Enhancers	Spleen	Spleen
20	chr12:11652800-11653600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:11652800-11653800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:11652800-11653800	Enhancers	Esophagus	oesophagus
23	chr12:11652800-11654000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
24	chr12:11652800-11654000	Enhancers	Fetal Brain Male	brain
25	chr12:11652800-11654000	Enhancers	Gastric	stomach
26	chr12:11652800-11654000	Enhancers	Pancreas	Pancrea
27	chr12:11652800-11654000	Enhancers	Right Ventricle	heart
28	chr12:11652800-11654200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:11652800-11654200	Bivalent/Poised TSS	Fetal Brain Female	brain

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