Variant report

Variant	rs4653718
Chromosome Location	chr1:226336163-226336164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226313181..226318051-chr1:226333070..226339347,8	MCF-7	breast:
2	chr1:226321090..226323803-chr1:226336056..226338005,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270598	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10732276	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10799337	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10799340	0.88[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10915952	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10915953	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10915954	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap]
rs12032630	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12047894	0.84[EUR][1000 genomes]
rs12136759	0.82[MEX][hapmap]
rs2306121	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2889539	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3914142	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653722	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9286997	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9286998	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9659225	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9659397	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9660696	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9660874	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9660924	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9661836	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9662709	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9725308	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9725342	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9728014	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9728310	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9729232	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9729554	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4653718	ACBD3	cis	normal skin	skin_eQTL
rs4653718	PARP1	cis	cerebellum	SCAN
rs4653718	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226323200-226344600	Weak transcription	Brain Angular Gyrus	brain
2	chr1:226323400-226338400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:226323600-226338400	Weak transcription	Fetal Kidney	kidney
4	chr1:226323600-226339800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:226323600-226339800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:226323600-226346000	Weak transcription	Fetal Heart	heart
7	chr1:226323800-226338600	Weak transcription	Fetal Brain Male	brain
8	chr1:226323800-226355000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:226324000-226339800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:226324000-226340000	Weak transcription	Stomach Mucosa	stomach
11	chr1:226324000-226372800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:226324400-226339800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:226324400-226346200	Weak transcription	Pancreas	Pancrea
14	chr1:226329600-226353800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:226330000-226341000	Weak transcription	Psoas Muscle	Psoas
16	chr1:226330600-226354200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:226330800-226336800	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:226330800-226337400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr1:226330800-226354200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:226331000-226336800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:226331000-226337000	Strong transcription	HSMM	muscle
22	chr1:226331000-226341600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:226331000-226353800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:226331000-226353800	Strong transcription	Adipose Nuclei	Adipose
25	chr1:226331000-226354000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:226331000-226355200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:226331200-226336800	Strong transcription	Placenta	Placenta
28	chr1:226331200-226337000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:226331200-226342400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:226331200-226342600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr1:226331600-226336800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:226331600-226338400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:226331600-226340000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:226331600-226342200	Strong transcription	Osteobl	bone
35	chr1:226331600-226342400	Strong transcription	Primary B cells from cord blood	blood
36	chr1:226331600-226342600	Strong transcription	NH-A	brain
37	chr1:226331600-226342800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:226331600-226342800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:226331600-226342800	Strong transcription	Fetal Lung	lung
40	chr1:226331600-226343000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:226331600-226346200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:226331600-226353600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:226331600-226353800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr1:226331600-226354200	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:226331600-226355600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr1:226331800-226336200	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr1:226331800-226336600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:226331800-226336600	Strong transcription	Dnd41	blood
49	chr1:226331800-226336800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:226331800-226337000	Strong transcription	NHDF-Ad	bronchial

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