Variant report

Variant	rs12594474
Chromosome Location	chr15:93503827-93503828
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:93502784..93504622-chr15:93520674..93522554,2	MCF-7	breast:
2	chr15:93503187..93507973-chr15:93511810..93515580,5	K562	blood:

Variant related genes	Relation type
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10520718	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1074512	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11074120	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11634566	0.82[AMR][1000 genomes]
rs11857466	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857669	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12591124	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592920	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12594991	0.82[AMR][1000 genomes]
rs12914956	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17610487	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1881834	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1881835	0.80[AMR][1000 genomes]
rs2388055	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34448107	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36032658	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3736619	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3784785	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3826035	0.82[AMR][1000 genomes]
rs62023146	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6497011	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6497013	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7174043	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7176652	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7179863	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8026679	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8042395	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8042632	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9302362	0.90[AMR][1000 genomes];0.92[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	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
rs12594474	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	chr15:93493000-93508600	Strong transcription	Hela-S3	cervix
2	chr15:93493200-93504400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:93493200-93504800	Strong transcription	Fetal Kidney	kidney
4	chr15:93493200-93508200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:93493200-93512200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:93493200-93533000	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:93493200-93536000	Strong transcription	HSMM	muscle
8	chr15:93493200-93571000	Strong transcription	Dnd41	blood
9	chr15:93493200-93571200	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr15:93493400-93504800	Strong transcription	Brain Anterior Caudate	brain
11	chr15:93493400-93505000	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:93493400-93505800	Strong transcription	Fetal Lung	lung
13	chr15:93493400-93508200	Strong transcription	Primary B cells from cord blood	blood
14	chr15:93493400-93508400	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:93493400-93511800	Strong transcription	Adipose Nuclei	Adipose
16	chr15:93493400-93511800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr15:93493400-93548000	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr15:93493400-93568600	Strong transcription	Liver	Liver
19	chr15:93493400-93569600	Strong transcription	Placenta	Placenta
20	chr15:93493400-93571000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:93493400-93571000	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr15:93493600-93504800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr15:93493600-93510600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:93493600-93521600	Strong transcription	Osteobl	bone
25	chr15:93493600-93523400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:93493600-93571400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:93493800-93505000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr15:93493800-93508200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr15:93493800-93508200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr15:93493800-93522400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr15:93493800-93532600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:93493800-93561400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr15:93493800-93571400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:93494000-93504000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:93494000-93505600	Strong transcription	GM12878-XiMat	blood
36	chr15:93494000-93508200	Strong transcription	Fetal Intestine Large	intestine
37	chr15:93494000-93508200	Strong transcription	NHEK	skin
38	chr15:93494000-93508600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:93494000-93512400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr15:93494000-93512600	Weak transcription	Aorta	Aorta
41	chr15:93494000-93520800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:93494000-93568200	Strong transcription	Fetal Thymus	thymus
43	chr15:93494000-93570400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:93494000-93570800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:93494000-93571000	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:93494000-93571400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:93494200-93505400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:93494200-93505600	Strong transcription	A549	lung
49	chr15:93494200-93506200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:93494200-93512400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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