Variant report

Variant	rs2254142
Chromosome Location	chr15:93186729-93186730
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93064927..93066555-chr15:93186642..93188513,2	MCF-7	breast:
2	chr15:93080164..93082598-chr15:93185700..93188569,2	MCF-7	breast:
3	chr15:93017434..93020038-chr15:93186293..93188824,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12443091	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs12593636	1.00[ASN][1000 genomes]
rs12908852	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs1496712	0.91[EUR][1000 genomes]
rs1496726	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs16947098	1.00[ASN][1000 genomes]
rs16947102	1.00[ASN][1000 genomes]
rs16974307	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs184048	0.87[EUR][1000 genomes]
rs2453901	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs285754	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285755	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285757	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285758	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285766	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs285772	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366789	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373481	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs406032	0.87[EUR][1000 genomes]
rs413450	0.89[EUR][1000 genomes]
rs426221	1.00[ASN][1000 genomes]
rs434826	0.83[EUR][1000 genomes]
rs503112	0.89[EUR][1000 genomes]
rs6496969	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs7178546	0.92[EUR][1000 genomes]
rs72758232	1.00[ASN][1000 genomes]
rs72758234	1.00[ASN][1000 genomes]
rs72758301	1.00[ASN][1000 genomes]
rs73454725	1.00[ASN][1000 genomes]
rs73454730	1.00[ASN][1000 genomes]
rs893379	0.88[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	esv1808537	chr15:93146057-93191935	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2254142	LOC400451	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93171000-93197400	Weak transcription	Primary T cells from cord blood	blood
2	chr15:93178000-93188400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:93178800-93187600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:93180200-93187200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:93181200-93187800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:93181800-93187000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:93182000-93187000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:93182000-93197800	Weak transcription	Small Intestine	intestine
9	chr15:93182200-93187400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:93182400-93186800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:93182400-93187400	Weak transcription	Right Atrium	heart
12	chr15:93182400-93188400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:93182400-93188400	Weak transcription	Fetal Lung	lung
14	chr15:93182400-93190600	Weak transcription	Psoas Muscle	Psoas
15	chr15:93182400-93191200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:93182600-93187200	Weak transcription	Esophagus	oesophagus
17	chr15:93182600-93187400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:93182600-93187400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr15:93182600-93187600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:93182600-93197200	Weak transcription	Fetal Kidney	kidney
21	chr15:93183000-93188200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:93183200-93186800	Weak transcription	Gastric	stomach
23	chr15:93183200-93186800	Weak transcription	Pancreas	Pancrea
24	chr15:93183200-93187000	Weak transcription	Lung	lung
25	chr15:93183200-93187400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:93183200-93198400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:93183400-93186800	Weak transcription	Stomach Mucosa	stomach
28	chr15:93183600-93187400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:93186000-93188400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:93186000-93190600	Weak transcription	Fetal Intestine Small	intestine
31	chr15:93186200-93186800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:93186200-93188200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:93186400-93189400	Enhancers	Placenta	Placenta
34	chr15:93186400-93194200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr15:93186600-93187200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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