Variant report

Variant	rs260534
Chromosome Location	chr15:29983229-29983230
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:29983051..29984598-chr15:30024023..30026061,2	MCF-7	breast:
2	chr15:29978882..29981352-chr15:29982247..29985034,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104067	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10152681	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11073218	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12438925	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1383315	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap]
rs1480503	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs1552077	0.89[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs1679647	0.89[ASN][1000 genomes]
rs17750802	0.88[CHB][hapmap]
rs1871678	0.80[ASN][1000 genomes]
rs2032	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2229518	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2306437	0.88[CHB][hapmap]
rs2337167	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs260528	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260538	0.84[ASN][1000 genomes]
rs2878893	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2878905	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3809503	0.88[CHB][hapmap]
rs4073316	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4362339	0.89[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4779670	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs4780259	0.89[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4780260	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs7176476	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs7176594	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7180387	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs767514	1.00[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs785445	1.00[CHB][hapmap];0.90[JPT][hapmap]

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	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv903747	chr15:29361126-30008977	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv974492	chr15:29981646-29991999	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv18527	chr15:29983142-29983647	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29969200-29992000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:29972800-29989200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:29973600-29989600	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:29977800-29996200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:29978400-29990400	Weak transcription	NHLF	lung
6	chr15:29978600-29983400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:29978600-29984800	Weak transcription	NHDF-Ad	bronchial
8	chr15:29979200-29988400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:29979800-29993000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:29980800-29989800	Weak transcription	Brain Substantia Nigra	brain
11	chr15:29980800-29989800	Weak transcription	Fetal Kidney	kidney
12	chr15:29980800-29996400	Weak transcription	Colonic Mucosa	Colon
13	chr15:29981000-29990400	Weak transcription	Lung	lung
14	chr15:29981000-29990600	Weak transcription	Fetal Intestine Large	intestine
15	chr15:29981000-29994400	Weak transcription	Fetal Intestine Small	intestine
16	chr15:29981200-29989600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:29981200-29993000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:29981400-29991800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:29981400-29994800	Weak transcription	K562	blood
20	chr15:29981400-29996400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:29981600-29990400	Weak transcription	Esophagus	oesophagus
22	chr15:29981600-29990400	Weak transcription	Placenta	Placenta
23	chr15:29982000-29992000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr15:29982800-29983600	Enhancers	Stomach Mucosa	stomach
25	chr15:29982800-29983600	Enhancers	NH-A	brain
26	chr15:29982800-29983800	Enhancers	Pancreas	Pancrea
27	chr15:29982800-29984000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:29982800-29984200	Enhancers	Liver	Liver
29	chr15:29983000-29983600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:29983000-29983800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:29983000-29983800	Strong transcription	Stomach Smooth Muscle	stomach
32	chr15:29983000-29984000	Enhancers	HepG2	liver
33	chr15:29983000-29989600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:29983200-29983400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr15:29983200-29983400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:29983200-29983400	Enhancers	A549	lung
37	chr15:29983200-29983400	Strong transcription	HSMMtube	muscle
38	chr15:29983200-29983600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:29983200-29983600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:29983200-29983600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:29983200-29983600	Enhancers	Osteobl	bone
42	chr15:29983200-29983800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:29983200-29983800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr15:29983200-29983800	Enhancers	HMEC	breast
45	chr15:29983200-29983800	Enhancers	HSMM	muscle
46	chr15:29983200-29983800	Enhancers	HUVEC	blood vessel
47	chr15:29983200-29983800	Enhancers	NHEK	skin
48	chr15:29983200-29984000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:29983200-29984000	Enhancers	Gastric	stomach

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