Variant report

Variant	rs12904435
Chromosome Location	chr15:51110203-51110204
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51110106..51113018-chr15:51115605..51118067,2	K562	blood:
2	chr15:50978318..50980031-chr15:51108674..51110331,2	MCF-7	breast:
3	chr15:51056091..51061159-chr15:51107004..51114924,11	MCF-7	breast:
4	chr15:51090561..51092703-chr15:51108354..51111264,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092439	Chromatin interaction
ENSG00000138600	Chromatin interaction
ENSG00000241130	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11070812	0.84[ASN][1000 genomes]
rs11070822	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1135397	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs1147132	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1147134	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1147138	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1147140	0.86[ASN][1000 genomes]
rs11636886	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12050528	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12148865	0.86[ASN][1000 genomes]
rs12440081	0.85[ASN][1000 genomes]
rs12440167	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12440387	0.90[AFR][1000 genomes]
rs12440570	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs12440745	0.86[AFR][1000 genomes]
rs12440864	0.89[JPT][hapmap]
rs12442145	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs12591438	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12592178	0.94[ASN][1000 genomes]
rs12592778	0.82[CHB][hapmap]
rs12593342	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12593765	0.90[AFR][1000 genomes]
rs12593778	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap]
rs12595051	0.92[ASN][1000 genomes]
rs12595200	0.87[ASN][1000 genomes]
rs12595526	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1276855	0.82[ASN][1000 genomes]
rs1276856	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12899428	0.90[ASN][1000 genomes]
rs1290084	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12902649	0.85[AFR][1000 genomes]
rs12909760	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12909839	0.90[AFR][1000 genomes]
rs12911207	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12916845	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17646025	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs17646461	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17646917	0.90[AFR][1000 genomes]
rs17702978	0.83[ASN][1000 genomes]
rs1871460	0.90[AFR][1000 genomes]
rs1876784	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1903588	0.89[ASN][1000 genomes]
rs1903589	0.83[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1904430	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes]
rs1955	0.90[AFR][1000 genomes]
rs2289304	0.86[CEU][hapmap]
rs2291107	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2414057	0.86[ASN][1000 genomes]
rs2414063	0.85[CHB][hapmap]
rs2574754	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2574756	0.94[ASN][1000 genomes]
rs2614762	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2614765	0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2614766	0.87[ASN][1000 genomes]
rs2614768	0.87[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2614774	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2614788	0.95[AFR][1000 genomes]
rs2614793	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2619689	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2619690	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2619695	0.88[ASN][1000 genomes]
rs2619696	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2663528	0.82[ASN][1000 genomes]
rs2663530	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2663531	0.95[AFR][1000 genomes]
rs2663532	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2663536	0.81[ASN][1000 genomes]
rs2663540	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2663542	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2663552	0.89[ASN][1000 genomes]
rs2663557	0.82[AFR][1000 genomes]
rs28565448	0.89[ASN][1000 genomes]
rs34991408	0.83[ASN][1000 genomes]
rs35088194	0.85[ASN][1000 genomes]
rs35473969	0.88[ASN][1000 genomes]
rs35573737	0.90[AFR][1000 genomes]
rs35862680	0.89[ASN][1000 genomes]
rs36004063	0.90[AFR][1000 genomes]
rs3784304	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3825798	0.86[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs3848132	0.80[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4142324	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs56108218	0.85[ASN][1000 genomes]
rs57262951	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59486015	0.80[AFR][1000 genomes]
rs67889301	0.88[AFR][1000 genomes]
rs7179527	0.80[AFR][1000 genomes]
rs7181593	0.91[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7183420	0.80[ASN][1000 genomes]
rs72742342	0.92[ASN][1000 genomes]
rs737031	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8033807	0.85[ASN][1000 genomes]
rs8042982	0.85[ASN][1000 genomes]
rs8043017	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs8182062	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs936482	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053966	chr15:50715572-51133186	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats 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	65 gene(s)	inside rSNPs	diseases
2	nsv542383	chr15:50715572-51133186	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv1051990	chr15:50745814-51133186	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	nsv1048621	chr15:50775451-51115535	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	nsv1055112	chr15:50822035-51133186	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	46 gene(s)	inside rSNPs	diseases
18	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
19	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
20	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
21	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
22	nsv904212	chr15:50979738-51132170	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
23	nsv904213	chr15:51011402-51119731	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
24	nsv457137	chr15:51019117-51117524	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
25	nsv569402	chr15:51019117-51117524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
26	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51107000-51112000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:51108800-51110400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:51108800-51112000	Weak transcription	Psoas Muscle	Psoas
4	chr15:51108800-51112600	Enhancers	Hela-S3	cervix
5	chr15:51108800-51116600	Weak transcription	Fetal Lung	lung
6	chr15:51109000-51112000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:51109800-51110400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:51109800-51110600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:51109800-51110600	Enhancers	HSMMtube	muscle
10	chr15:51110000-51111000	Enhancers	HSMM	muscle
11	chr15:51110000-51112200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:51110200-51110400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr15:51110200-51110600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr15:51110200-51110600	Bivalent Enhancer	Osteobl	bone

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