Variant report

Variant	rs12490889
Chromosome Location	chr3:51405765-51405766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51404406..51407257-chr3:51420793..51424022,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145050	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10510757	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10510758	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12485610	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12487426	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12487468	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489219	0.81[AMR][1000 genomes]
rs12489414	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490471	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12491048	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12492624	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12493265	0.88[ASN][1000 genomes]
rs12493618	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12493857	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12493978	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12494462	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12494979	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13089799	0.85[ASN][1000 genomes]
rs13090348	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1370124	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17051783	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17051811	0.85[ASN][1000 genomes]
rs17661242	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17712228	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1842394	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2033703	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2082992	0.89[ASN][1000 genomes]
rs2082993	0.87[ASN][1000 genomes]
rs2170177	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2217938	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241785	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304512	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306430	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355946	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2356261	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2356298	0.89[ASN][1000 genomes]
rs35536327	0.85[ASN][1000 genomes]
rs3749317	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3792408	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3804766	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3828395	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4468966	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687553	0.87[ASN][1000 genomes]
rs4687563	0.87[ASN][1000 genomes]
rs4687601	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687605	0.89[ASN][1000 genomes]
rs4687610	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4687656	0.89[ASN][1000 genomes]
rs4687691	0.86[ASN][1000 genomes]
rs4687731	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687777	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687794	0.86[ASN][1000 genomes]
rs4687803	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4687804	0.84[AMR][1000 genomes]
rs4687811	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687812	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687813	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974098	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55667499	0.87[ASN][1000 genomes]
rs55671465	0.81[ASN][1000 genomes]
rs56239081	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56729479	0.89[ASN][1000 genomes]
rs57027950	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57047724	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57603251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57700326	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57831708	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58059174	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58201844	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58568178	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58836277	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59129045	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59563413	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59838596	0.88[ASN][1000 genomes]
rs59953568	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60606339	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61233013	0.86[ASN][1000 genomes]
rs61419317	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61689323	0.88[ASN][1000 genomes]
rs72936462	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72945708	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72945713	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72951443	0.88[ASN][1000 genomes]
rs73834252	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73834253	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73834254	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73834258	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73837435	0.86[EUR][1000 genomes]
rs73837436	0.86[EUR][1000 genomes]
rs73837437	0.86[EUR][1000 genomes]
rs73837438	0.86[EUR][1000 genomes]
rs73837439	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73837442	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73837443	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs751076	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7642698	0.88[ASN][1000 genomes]
rs880478	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817077	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9817872	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9819195	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9820140	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9827186	0.85[ASN][1000 genomes]
rs9829057	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9842600	0.86[ASN][1000 genomes]
rs9843583	0.86[ASN][1000 genomes]
rs9856134	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9861019	0.82[ASN][1000 genomes]
rs9872991	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv460534	chr3:51393046-51416108	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv590274	chr3:51393046-51416108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv460535	chr3:51395571-51416108	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv590275	chr3:51395571-51416108	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
3	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
4	chr3:51384200-51420600	Weak transcription	Fetal Brain Male	brain
5	chr3:51391600-51406800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:51392800-51418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:51398800-51405800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:51400600-51411400	Weak transcription	Brain Anterior Caudate	brain
9	chr3:51400800-51408200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:51400800-51410800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:51400800-51411000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:51400800-51411400	Weak transcription	Brain Substantia Nigra	brain
13	chr3:51400800-51411400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:51400800-51412200	Weak transcription	HSMMtube	muscle
15	chr3:51401000-51411800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:51404800-51406400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr3:51405400-51406000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
18	chr3:51405400-51406000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
19	chr3:51405400-51406000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr3:51405400-51406000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:51405400-51406200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:51405400-51406400	Strong transcription	Brain Hippocampus Middle	brain
23	chr3:51405600-51405800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
24	chr3:51405600-51405800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:51405600-51405800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr3:51405600-51405800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
27	chr3:51405600-51405800	ZNF genes & repeats	Brain Germinal Matrix	brain
28	chr3:51405600-51406000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:51405600-51406000	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
30	chr3:51405600-51406000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
31	chr3:51405600-51406000	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:51405600-51406000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
33	chr3:51405600-51406200	Strong transcription	Fetal Brain Female	brain
34	chr3:51405600-51406400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
35	chr3:51405600-51409000	Strong transcription	Brain Angular Gyrus	brain

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