Variant report

Variant	rs2959041
Chromosome Location	chr15:31329142-31329143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31326150..31329950-chr15:31331273..31334217,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAN1-1	chr15:31328656-31329566	NONHSAT041422

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10162731	1.00[ASN][1000 genomes]
rs1035705	0.85[ASN][1000 genomes]
rs1035706	0.90[ASN][1000 genomes]
rs10851487	0.85[ASN][1000 genomes]
rs11070764	0.85[ASN][1000 genomes]
rs11070767	0.84[ASN][1000 genomes]
rs11636071	0.97[ASN][1000 genomes]
rs11636121	0.85[ASN][1000 genomes]
rs1991214	0.85[ASN][1000 genomes]
rs2278133	0.81[ASN][1000 genomes]
rs2288241	0.85[ASN][1000 genomes]
rs2288242	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2338834	1.00[ASN][1000 genomes]
rs2338835	0.85[ASN][1000 genomes]
rs2911849	0.85[ASN][1000 genomes]
rs2911850	0.85[ASN][1000 genomes]
rs2911851	0.85[ASN][1000 genomes]
rs2911853	0.85[ASN][1000 genomes]
rs2911854	0.85[ASN][1000 genomes]
rs2959042	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743234	0.85[ASN][1000 genomes]
rs4779501	0.96[ASN][1000 genomes]
rs4779808	1.00[ASN][1000 genomes]
rs4779810	0.96[ASN][1000 genomes]
rs4779811	0.81[ASN][1000 genomes]
rs4779812	0.90[ASN][1000 genomes]
rs4779813	0.84[ASN][1000 genomes]
rs7165995	0.96[ASN][1000 genomes]
rs7173280	1.00[ASN][1000 genomes]
rs7173932	1.00[ASN][1000 genomes]
rs7174338	1.00[ASN][1000 genomes]
rs7174872	0.96[ASN][1000 genomes]
rs7179304	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037421	0.96[ASN][1000 genomes]
rs8041204	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
12	nsv903835	chr15:31312743-31384797	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31316800-31330000	Weak transcription	Pancreas	Pancrea
2	chr15:31317400-31334200	Weak transcription	Gastric	stomach
3	chr15:31324800-31332600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:31324800-31332800	Enhancers	Placenta	Placenta
5	chr15:31326000-31332200	Weak transcription	Spleen	Spleen
6	chr15:31326600-31329600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:31326800-31330000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:31326800-31339200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:31326800-31342800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:31327000-31331000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr15:31328400-31329400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:31328800-31329400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:31328800-31329600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:31328800-31334600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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