Variant report

Variant	rs13196905
Chromosome Location	chr6:2429573-2429574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:2429452..2431955-chr6:2435329..2437975,2	K562	blood:
2	chr6:2424842..2426390-chr6:2428236..2430027,2	MCF-7	breast:
3	chr6:2429452..2431211-chr6:2436475..2439136,2	K562	blood:

Variant related genes	Relation type
ENSG00000272465	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12197998	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs12213061	0.81[EUR][1000 genomes]
rs1883590	0.81[EUR][1000 genomes]
rs2092403	0.81[EUR][1000 genomes]
rs2281251	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959184	0.82[AFR][1000 genomes]
rs4959660	0.81[EUR][1000 genomes]
rs4959664	0.82[CHD][hapmap];0.87[GIH][hapmap];0.80[EUR][1000 genomes]
rs6920321	0.81[EUR][1000 genomes]
rs6940450	0.81[EUR][1000 genomes]
rs761098	0.91[CHB][hapmap];0.87[MEX][hapmap]
rs7755460	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13196905	TUBB2A	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2399800-2449200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:2402200-2449200	Weak transcription	Left Ventricle	heart
3	chr6:2414600-2434600	Weak transcription	Fetal Intestine Small	intestine
4	chr6:2414600-2452000	Weak transcription	Ovary	ovary
5	chr6:2414800-2448800	Weak transcription	Liver	Liver
6	chr6:2414800-2449200	Weak transcription	Fetal Stomach	stomach
7	chr6:2417600-2454200	Weak transcription	Pancreas	Pancrea
8	chr6:2426400-2439800	Weak transcription	Aorta	Aorta
9	chr6:2427800-2429600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:2427800-2429600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:2427800-2429600	Weak transcription	HSMM	muscle
12	chr6:2427800-2429800	Weak transcription	Osteobl	bone
13	chr6:2427800-2432000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:2427800-2432000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:2427800-2432000	Weak transcription	NH-A	brain
16	chr6:2427800-2432000	Weak transcription	NHDF-Ad	bronchial
17	chr6:2428000-2432000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:2428400-2431400	Weak transcription	HMEC	breast
19	chr6:2428800-2430000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:2428800-2446200	Weak transcription	Right Ventricle	heart
21	chr6:2429200-2429800	Enhancers	Esophagus	oesophagus
22	chr6:2429200-2430200	Enhancers	Placenta Amnion	Placenta Amnion

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