Variant report

Variant	rs10843490
Chromosome Location	chr12:29843391-29843392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10219522	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843479	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10843481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843484	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11050346	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11050350	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11050359	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11050361	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050365	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11050391	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11050396	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12368564	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1988266	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7135501	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs741613	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs741614	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs741615	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs741616	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs993994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3484985	chr12:29842885-29847783	Flanking Active TSS Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
4	nsv557918	chr12:29843095-29845324	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
5	nsv557919	chr12:29843095-29846017	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
6	nsv557920	chr12:29843095-29846251	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
7	nsv557921	chr12:29843095-29859352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29820200-29851600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:29820400-29844200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:29825400-29847800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:29828600-29854000	Weak transcription	Aorta	Aorta
5	chr12:29830000-29844000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:29830000-29854000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:29830000-29861600	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:29830200-29857400	Weak transcription	HSMM	muscle
9	chr12:29830400-29857400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:29830600-29858000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:29830800-29862600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:29831400-29850400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:29835000-29846800	Weak transcription	Right Ventricle	heart
14	chr12:29837600-29864200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:29837800-29844000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:29838000-29851800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:29839400-29858400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:29840200-29844200	Weak transcription	HMEC	breast
19	chr12:29840600-29859000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:29840800-29843800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:29842000-29847800	Weak transcription	Psoas Muscle	Psoas
22	chr12:29842200-29847000	Weak transcription	Fetal Heart	heart
23	chr12:29842400-29847600	Weak transcription	Left Ventricle	heart
24	chr12:29842600-29845600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:29842800-29843800	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr12:29842800-29844000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr12:29842800-29844800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:29843000-29843800	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr12:29843000-29845200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr12:29843200-29845200	Enhancers	HUES64 Cell Line	embryonic stem cell

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