Variant report

Variant	rs2878905
Chromosome Location	chr15:30101239-30101240
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	chr15:30099589..30102361-chr15:30114186..30117139,2	MCF-7	breast:
2	chr15:30099510..30101653-chr15:30102789..30104462,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259523	Chromatin interaction
ENSG00000104067	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10152681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10775231	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11073205	0.90[EUR][1000 genomes]
rs11073218	0.90[JPT][hapmap]
rs11636849	0.83[CEU][hapmap]
rs12438925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12440211	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12440708	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12441554	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1383315	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1480503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1552077	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1585900	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1679647	0.83[ASN][1000 genomes]
rs17750802	0.89[CHB][hapmap]
rs1871678	0.80[ASN][1000 genomes]
rs2032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2229518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306437	0.89[CHB][hapmap]
rs2337167	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs260531	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs260532	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs260533	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs260534	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs260535	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs28675809	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2878893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3809503	0.89[CHB][hapmap]
rs4073316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4362339	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4779670	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4780258	0.81[ASN][1000 genomes]
rs4780259	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4780260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4780263	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6495890	0.87[EUR][1000 genomes]
rs6495914	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495927	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495935	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495945	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7166786	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7168919	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7170406	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7171815	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175819	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7176476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176594	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7180387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs785445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023974	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8027827	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	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
6	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
7	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv1851951	chr15:30043659-30178871	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	esv1845759	chr15:30097078-30142373	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30058600-30106000	Weak transcription	Gastric	stomach
2	chr15:30065200-30103400	Weak transcription	Placenta	Placenta
3	chr15:30065600-30108200	Weak transcription	Pancreas	Pancrea
4	chr15:30082400-30113600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:30086000-30107600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:30091800-30108000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:30092600-30111400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:30093000-30107600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:30093400-30102600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:30093400-30102800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:30094600-30107600	Weak transcription	Left Ventricle	heart
12	chr15:30095200-30107000	Weak transcription	Fetal Intestine Small	intestine
13	chr15:30097200-30103800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:30097600-30104000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:30097600-30104200	Weak transcription	Fetal Kidney	kidney
16	chr15:30097600-30104400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:30097800-30103800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:30097800-30104000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:30097800-30104200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:30097800-30107600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:30098000-30102600	Weak transcription	Aorta	Aorta
22	chr15:30098000-30102600	Weak transcription	Brain Angular Gyrus	brain
23	chr15:30098000-30102800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:30098000-30103800	Weak transcription	HMEC	breast
25	chr15:30098000-30104200	Weak transcription	NHEK	skin
26	chr15:30098000-30104400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:30098000-30106400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr15:30098000-30107600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:30098000-30111600	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:30098000-30112400	Weak transcription	Fetal Stomach	stomach
31	chr15:30098200-30102800	Weak transcription	HepG2	liver
32	chr15:30098200-30103200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:30098200-30103800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr15:30098200-30103800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:30098200-30104000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:30098200-30104200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:30098200-30104400	Weak transcription	HUVEC	blood vessel
38	chr15:30098200-30104600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:30098200-30105000	Weak transcription	HSMM	muscle
40	chr15:30098200-30105800	Weak transcription	Right Atrium	heart
41	chr15:30098200-30107600	Weak transcription	Ovary	ovary
42	chr15:30098400-30104000	Weak transcription	Osteobl	bone
43	chr15:30098400-30111600	Weak transcription	HSMMtube	muscle
44	chr15:30098600-30103800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:30098600-30104800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:30098800-30102800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:30098800-30103400	Weak transcription	Small Intestine	intestine
48	chr15:30098800-30104600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:30098800-30104600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:30099000-30102400	Weak transcription	Brain Inferior Temporal Lobe	brain

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