Variant report

Variant	rs17646461
Chromosome Location	chr15:51158110-51158111
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	chr15:51056355..51060278-chr15:51155498..51158542,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138600	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11070822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1124769	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes]
rs1135397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1147132	0.93[ASN][1000 genomes]
rs1147134	0.93[ASN][1000 genomes]
rs1147137	0.87[ASN][1000 genomes]
rs1147138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1147140	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636886	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12050528	0.86[ASN][1000 genomes]
rs12440167	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12440387	0.88[ASN][1000 genomes]
rs12440570	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs12440745	0.89[ASN][1000 genomes]
rs12440864	0.89[JPT][hapmap]
rs12442145	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs12443062	1.00[AFR][1000 genomes]
rs12591438	0.92[ASN][1000 genomes]
rs12592178	0.83[ASN][1000 genomes]
rs12592778	0.82[CHB][hapmap]
rs12593342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12593765	0.90[ASN][1000 genomes]
rs12593778	0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs12595051	0.82[ASN][1000 genomes]
rs12595526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1276855	0.92[ASN][1000 genomes]
rs1276856	0.88[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1290083	0.82[ASN][1000 genomes]
rs1290084	0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs12904435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12909760	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909839	0.84[ASN][1000 genomes]
rs12911207	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12916845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17646025	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs17646917	0.84[ASN][1000 genomes]
rs17647040	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs17702978	0.93[ASN][1000 genomes]
rs1871460	0.89[ASN][1000 genomes]
rs1876784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1903588	0.85[ASN][1000 genomes]
rs1903589	0.83[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1904430	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1955	0.89[ASN][1000 genomes]
rs2289304	0.84[ASN][1000 genomes]
rs2291107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2574754	0.89[ASN][1000 genomes]
rs2574756	0.92[ASN][1000 genomes]
rs2614762	0.85[ASN][1000 genomes]
rs2614765	0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2614766	0.84[ASN][1000 genomes]
rs2614768	0.87[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2614771	0.84[ASN][1000 genomes]
rs2614774	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2614775	0.85[ASN][1000 genomes]
rs2614787	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2614788	0.89[ASN][1000 genomes]
rs2614793	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2619689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2619690	0.93[ASN][1000 genomes]
rs2619692	0.90[ASN][1000 genomes]
rs2619695	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619696	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2663528	0.92[ASN][1000 genomes]
rs2663530	0.90[ASN][1000 genomes]
rs2663531	0.89[ASN][1000 genomes]
rs2663532	0.93[ASN][1000 genomes]
rs2663536	0.92[ASN][1000 genomes]
rs2663540	0.92[ASN][1000 genomes]
rs2663542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2663552	0.85[ASN][1000 genomes]
rs2663557	0.89[ASN][1000 genomes]
rs35573737	0.89[ASN][1000 genomes]
rs36004063	0.87[ASN][1000 genomes]
rs3784304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3825797	0.89[ASN][1000 genomes]
rs3825798	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3848132	0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4142324	0.88[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs67889301	0.88[ASN][1000 genomes]
rs71426053	0.80[ASN][1000 genomes]
rs7170036	0.83[ASN][1000 genomes]
rs7170302	0.88[ASN][1000 genomes]
rs7170310	0.88[ASN][1000 genomes]
rs7176498	0.80[ASN][1000 genomes]
rs7181593	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs72742342	0.82[ASN][1000 genomes]
rs737031	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs8043017	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8182062	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs936482	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv457134	chr15:50770868-51184583	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv471242	chr15:50770868-51184583	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv569396	chr15:50770868-51184583	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv457135	chr15:50770868-51189707	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv569397	chr15:50770868-51189707	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	nsv1047039	chr15:50782070-51187804	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
10	nsv542385	chr15:50782070-51187804	Weak transcription Enhancers Strong transcription Active TSS 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 target site	54 gene(s)	inside rSNPs	diseases
11	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
12	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
13	nsv1042372	chr15:50846461-51208891	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
14	nsv542386	chr15:50846461-51208891	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
15	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
16	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
17	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
18	nsv516168	chr15:51114437-51217361	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51147800-51165800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:51151200-51177400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:51156600-51158600	Enhancers	Fetal Intestine Large	intestine
4	chr15:51156800-51158600	Enhancers	Fetal Intestine Small	intestine
5	chr15:51157400-51158200	Enhancers	Fetal Kidney	kidney
6	chr15:51157800-51158400	Enhancers	Duodenum Mucosa	Duodenum
7	chr15:51157800-51165200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:51157800-51165800	Weak transcription	Rectal Mucosa Donor 29	rectum

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