Variant report

Variant	rs1343668
Chromosome Location	chr12:124412686-124412687
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124286094..124286683-chr12:124412581..124413486,2	MCF-7	breast:
2	chr12:124407933..124410247-chr12:124410271..124413252,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197653	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11829426	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11835416	1.00[MEX][hapmap]
rs12099459	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1873224	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs55680811	1.00[EUR][1000 genomes]
rs55996758	1.00[EUR][1000 genomes]
rs56169314	1.00[EUR][1000 genomes]
rs57352016	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57531416	1.00[EUR][1000 genomes]
rs58157153	0.81[AMR][1000 genomes]
rs58498731	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58556542	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58788131	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59002473	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59035549	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60560821	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60980349	1.00[EUR][1000 genomes]
rs61151021	1.00[EUR][1000 genomes]
rs61740383	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61749063	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7301547	1.00[EUR][1000 genomes]
rs73409428	1.00[EUR][1000 genomes]
rs7976904	1.00[EUR][1000 genomes]
rs939464	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs952631	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv1811815	chr12:124374716-124424636	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1832870	chr12:124374716-124424636	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv522321	chr12:124383950-124424636	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124393800-124418000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr12:124394200-124418400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:124400400-124417800	Weak transcription	Spleen	Spleen
4	chr12:124407400-124422000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:124408400-124418000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:124408800-124428000	Weak transcription	Right Atrium	heart
7	chr12:124409200-124414600	Weak transcription	Fetal Brain Female	brain
8	chr12:124409400-124419600	Weak transcription	Right Ventricle	heart
9	chr12:124409600-124426200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:124409800-124419400	Weak transcription	Brain Anterior Caudate	brain
11	chr12:124410000-124418600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:124410200-124418200	Weak transcription	Fetal Intestine Small	intestine
13	chr12:124410400-124413600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:124410400-124420600	Weak transcription	Pancreas	Pancrea
15	chr12:124410800-124419200	Weak transcription	Brain Substantia Nigra	brain
16	chr12:124410800-124420600	Weak transcription	Brain Angular Gyrus	brain
17	chr12:124411200-124420600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:124411800-124416200	Strong transcription	Brain Germinal Matrix	brain
19	chr12:124412000-124420400	Enhancers	Fetal Thymus	thymus
20	chr12:124412200-124413400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:124412400-124413200	Enhancers	Primary B cells from peripheral blood	blood
22	chr12:124412400-124415000	Enhancers	Fetal Muscle Leg	muscle
23	chr12:124412400-124416200	Enhancers	Thymus	Thymus
24	chr12:124412600-124413200	Bivalent Enhancer	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links