Variant report

Variant	rs4778062
Chromosome Location	chr15:93503062-93503063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93502784..93504622-chr15:93520674..93522554,2	MCF-7	breast:
2	chr15:93501140..93503509-chr15:93512727..93514419,2	K562	blood:
3	chr15:93500970..93503092-chr15:93504292..93507134,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10520717	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10520719	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11074126	0.82[AMR][1000 genomes]
rs11630052	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11630582	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11631553	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11632302	0.85[EUR][1000 genomes]
rs11632522	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11634204	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11634207	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11637047	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11637185	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11857145	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12594991	0.87[ASN][1000 genomes]
rs12906132	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12907579	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1534779	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17525800	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2033844	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272457	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2272459	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28668136	0.85[AMR][1000 genomes]
rs34026217	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35477598	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35596808	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs36048863	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3784786	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3817597	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4778065	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56358327	0.85[AMR][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	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
2	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
3	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
4	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4778062	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93478600-93503200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:93493000-93508600	Strong transcription	Hela-S3	cervix
3	chr15:93493200-93503800	Strong transcription	Brain Substantia Nigra	brain
4	chr15:93493200-93504400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:93493200-93504800	Strong transcription	Fetal Kidney	kidney
6	chr15:93493200-93508200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:93493200-93512200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:93493200-93533000	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:93493200-93536000	Strong transcription	HSMM	muscle
10	chr15:93493200-93571000	Strong transcription	Dnd41	blood
11	chr15:93493200-93571200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr15:93493400-93504800	Strong transcription	Brain Anterior Caudate	brain
13	chr15:93493400-93505000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr15:93493400-93505800	Strong transcription	Fetal Lung	lung
15	chr15:93493400-93508200	Strong transcription	Primary B cells from cord blood	blood
16	chr15:93493400-93508400	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:93493400-93511800	Strong transcription	Adipose Nuclei	Adipose
18	chr15:93493400-93511800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr15:93493400-93548000	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr15:93493400-93568600	Strong transcription	Liver	Liver
21	chr15:93493400-93569600	Strong transcription	Placenta	Placenta
22	chr15:93493400-93571000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:93493400-93571000	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr15:93493600-93504800	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr15:93493600-93510600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:93493600-93521600	Strong transcription	Osteobl	bone
27	chr15:93493600-93523400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:93493600-93571400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr15:93493800-93505000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr15:93493800-93508200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr15:93493800-93508200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr15:93493800-93522400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr15:93493800-93532600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:93493800-93561400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr15:93493800-93571400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:93494000-93503400	Strong transcription	Thymus	Thymus
37	chr15:93494000-93503800	Strong transcription	HMEC	breast
38	chr15:93494000-93504000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:93494000-93505600	Strong transcription	GM12878-XiMat	blood
40	chr15:93494000-93508200	Strong transcription	Fetal Intestine Large	intestine
41	chr15:93494000-93508200	Strong transcription	NHEK	skin
42	chr15:93494000-93508600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:93494000-93512400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr15:93494000-93512600	Weak transcription	Aorta	Aorta
45	chr15:93494000-93520800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:93494000-93568200	Strong transcription	Fetal Thymus	thymus
47	chr15:93494000-93570400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:93494000-93570800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:93494000-93571000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:93494000-93571400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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