Variant report

Variant	rs2588400
Chromosome Location	chr12:40873251-40873252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MUC19-1	chr12:40872855-40879178	NONHSAT027728

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10083205	0.87[GIH][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.91[YRI][hapmap]
rs10784705	0.87[GIH][hapmap];0.83[YRI][hapmap]
rs10878714	0.85[ASN][1000 genomes]
rs10878731	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11177226	0.87[GIH][hapmap];0.83[YRI][hapmap]
rs1492318	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1492319	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1602635	0.83[YRI][hapmap]
rs1838352	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1838353	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2588399	0.93[CEU][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs2920814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920820	0.81[JPT][hapmap]
rs2920821	0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs2920828	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2933352	0.94[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes]
rs2933357	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7487140	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7972739	0.82[YRI][hapmap]
rs7974188	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	esv1848303	chr12:40867011-40887238	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	esv1850439	chr12:40867211-40887867	Enhancers ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv20428	chr12:40867874-40884927	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	esv3390786	chr12:40871685-40877783	ZNF genes & repeats Weak transcription Strong transcription	lncRNA	n/a	inside rSNPs	diseases
6	esv3500652	chr12:40872785-40877883	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	inside rSNPs	diseases
7	nsv516022	chr12:40873026-40874088	ZNF genes & repeats Weak transcription Strong transcription	lncRNA	n/a	inside rSNPs	diseases
8	esv1827225	chr12:40873026-40894172	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv1833623	chr12:40873026-40894172	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv821471	chr12:40873057-40885132	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv16680	chr12:40873057-40885157	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	esv1816871	chr12:40873251-40875695	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
13	nsv511492	chr12:40873251-40876644	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40872800-40873600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
2	chr12:40872800-40873800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
3	chr12:40872800-40873800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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