Variant report

Variant	rs12496321
Chromosome Location	chr3:177411554-177411555
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:177407076..177409234-chr3:177410395..177412106,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10513747	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513748	0.86[ASN][1000 genomes]
rs10513749	0.84[CHB][hapmap]
rs10513750	0.84[CHB][hapmap]
rs10936953	0.94[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10936954	0.86[ASN][1000 genomes]
rs11915692	0.87[ASN][1000 genomes]
rs12487312	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12487458	0.84[CHB][hapmap]
rs12489304	0.84[CHB][hapmap]
rs12489969	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13059117	0.86[ASN][1000 genomes]
rs13059514	0.94[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13064192	0.92[ASN][1000 genomes]
rs13071785	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13074455	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13082519	0.84[CHB][hapmap]
rs13097562	0.93[ASN][1000 genomes]
rs13097723	0.80[ASN][1000 genomes]
rs13098037	0.93[ASN][1000 genomes]
rs1499809	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499810	0.82[ASN][1000 genomes]
rs1499811	0.95[ASN][1000 genomes]
rs1500047	0.84[ASN][1000 genomes]
rs1500048	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1604032	0.86[ASN][1000 genomes]
rs17635512	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17635597	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1846628	0.84[ASN][1000 genomes]
rs2062499	0.84[CHB][hapmap]
rs2062500	0.93[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34066617	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34188001	0.84[ASN][1000 genomes]
rs34347103	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34407557	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34491022	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34557886	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34638059	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34763113	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34992356	0.86[ASN][1000 genomes]
rs35110045	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35468531	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35610650	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35652846	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35830472	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35847814	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36055300	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4857725	0.80[ASN][1000 genomes]
rs4857726	0.80[ASN][1000 genomes]
rs56005554	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61541774	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6443481	0.86[ASN][1000 genomes]
rs6443482	0.84[ASN][1000 genomes]
rs66636257	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67189039	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765836	0.80[ASN][1000 genomes]
rs6779492	0.86[ASN][1000 genomes]
rs67797381	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793629	0.84[CHB][hapmap]
rs6798785	0.82[ASN][1000 genomes]
rs6803889	0.86[ASN][1000 genomes]
rs68151580	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71308158	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615900	0.82[ASN][1000 genomes]
rs7639373	0.84[CHB][hapmap]
rs7646117	0.82[ASN][1000 genomes]
rs7652174	0.86[ASN][1000 genomes]
rs937507	0.86[ASN][1000 genomes]
rs937561	0.82[ASN][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	esv2752972	chr3:176924298-177425298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv998537	chr3:177403421-177425648	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1009087	chr3:177405231-177422275	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177392400-177418800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:177395000-177411600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:177398800-177421600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:177405800-177411600	Weak transcription	Fetal Brain Male	brain
5	chr3:177406600-177412000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:177406800-177411600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:177406800-177411600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:177406800-177411800	Weak transcription	Brain Anterior Caudate	brain
9	chr3:177407000-177411600	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:177410600-177412000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:177411000-177413000	Enhancers	HUVEC	blood vessel
12	chr3:177411200-177412200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:177411200-177412800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:177411200-177413000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:177411200-177413000	Enhancers	Fetal Lung	lung
16	chr3:177411200-177413000	Enhancers	NHLF	lung
17	chr3:177411400-177412000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:177411400-177412000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:177411400-177412200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:177411400-177412200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:177411400-177412200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:177411400-177412800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr3:177411400-177413000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:177411400-177414400	Enhancers	Dnd41	blood

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