Variant report

Variant	rs4897243
Chromosome Location	chr6:128389074-128389075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:128388904-128389280	H1-hESC	embryonic stem cell:	n/a	chr6:128389086-128389099 chr6:128389088-128389097 chr6:128389088-128389097 chr6:128389086-128389097 chr6:128389088-128389097
2	CEBPB	chr6:128388901-128389275	A549	lung:	n/a	chr6:128389086-128389099 chr6:128389088-128389097 chr6:128389088-128389097 chr6:128389086-128389097 chr6:128389088-128389097
3	CEBPB	chr6:128388913-128389281	IMR90	lung:	n/a	chr6:128389086-128389099 chr6:128389088-128389097 chr6:128389088-128389097 chr6:128389086-128389097 chr6:128389088-128389097
4	CEBPB	chr6:128388951-128389226	K562	blood:	n/a	chr6:128389086-128389099 chr6:128389088-128389097 chr6:128389088-128389097 chr6:128389086-128389097 chr6:128389088-128389097
5	CEBPB	chr6:128388907-128389283	HepG2	liver:	n/a	chr6:128389086-128389099 chr6:128389088-128389097 chr6:128389088-128389097 chr6:128389086-128389097 chr6:128389088-128389097
6	CEBPB	chr6:128388818-128389242	MCF-7	breast:	n/a	chr6:128389086-128389099 chr6:128389088-128389097 chr6:128389088-128389097 chr6:128389086-128389097 chr6:128389088-128389097
7	CEBPB	chr6:128388950-128389181	A549	lung:	n/a	chr6:128389086-128389099 chr6:128389088-128389097 chr6:128389088-128389097 chr6:128389086-128389097 chr6:128389088-128389097
8	CEBPB	chr6:128388937-128389237	Hela-S3	cervix:	n/a	chr6:128389086-128389099 chr6:128389088-128389097 chr6:128389088-128389097 chr6:128389086-128389097 chr6:128389088-128389097
9	CEBPB	chr6:128389006-128389251	MCF-7	breast:	n/a	chr6:128389086-128389099 chr6:128389088-128389097 chr6:128389088-128389097 chr6:128389086-128389097 chr6:128389088-128389097
10	CEBPB	chr6:128388899-128389260	ECC-1	luminal epithelium:	n/a	chr6:128389086-128389099 chr6:128389088-128389097 chr6:128389088-128389097 chr6:128389086-128389097 chr6:128389088-128389097

Variant related genes	Relation type
PTPRK	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10046118	0.89[CEU][hapmap]
rs10046119	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs12661501	1.00[GIH][hapmap]
rs17055223	0.89[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs17055231	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs1883810	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs35335036	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4345415	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4377806	1.00[YRI][hapmap]
rs4475344	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs4544930	1.00[YRI][hapmap]
rs4598101	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4895829	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4897239	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4897240	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4897241	0.89[CEU][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4897242	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6569520	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs6569521	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6569522	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6569523	1.00[CEU][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6913095	0.84[CEU][hapmap]
rs6913595	0.95[EUR][1000 genomes]
rs6928445	0.89[CEU][hapmap]
rs6928496	0.89[CEU][hapmap]
rs6928512	0.89[CEU][hapmap]
rs6938574	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7756639	0.95[EUR][1000 genomes]
rs7757761	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7758689	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7769691	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7774703	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9321106	0.89[CEU][hapmap]
rs9321107	0.89[CEU][hapmap]
rs9321108	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9321109	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9321110	0.83[EUR][1000 genomes]
rs9375546	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9402016	0.89[EUR][1000 genomes]
rs9482857	0.89[EUR][1000 genomes]
rs9482858	0.94[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs9482859	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs9482860	0.94[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs9482861	0.89[CEU][hapmap]
rs9482862	0.89[CEU][hapmap]
rs9482863	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs9482864	0.89[CEU][hapmap]
rs9482865	0.89[CEU][hapmap]
rs9482866	0.89[CEU][hapmap]
rs9482868	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs9482871	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9482872	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9491904	0.89[CEU][hapmap]
rs9491906	0.89[CEU][hapmap]
rs970363	0.89[CEU][hapmap]
rs970364	0.94[CEU][hapmap];0.94[EUR][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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv604643	chr6:128359362-128493991	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4897243	GBP1	trans	brain	seeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128289000-128431000	Weak transcription	Psoas Muscle	Psoas
2	chr6:128347000-128405200	Weak transcription	Lung	lung
3	chr6:128350000-128401000	Weak transcription	Small Intestine	intestine
4	chr6:128367600-128398000	Weak transcription	HUVEC	blood vessel
5	chr6:128370000-128412600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:128372400-128412200	Weak transcription	Placenta	Placenta
7	chr6:128374600-128419400	Weak transcription	Esophagus	oesophagus
8	chr6:128375000-128419400	Weak transcription	Gastric	stomach
9	chr6:128375000-128433800	Weak transcription	Aorta	Aorta
10	chr6:128375600-128413000	Weak transcription	Colonic Mucosa	Colon
11	chr6:128377800-128403400	Weak transcription	Fetal Kidney	kidney
12	chr6:128378000-128390200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:128379000-128432800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:128379400-128390400	Weak transcription	NHDF-Ad	bronchial
15	chr6:128379400-128396600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:128379400-128412200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:128379600-128390000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:128379800-128389200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:128381800-128389200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:128383000-128389400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:128384000-128389600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr6:128384000-128396000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:128385000-128390800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:128385800-128406400	Weak transcription	Primary T cells from cord blood	blood
25	chr6:128385800-128419400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:128386400-128389600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr6:128387000-128389600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:128387200-128389400	Strong transcription	NH-A	brain
29	chr6:128387200-128389600	Strong transcription	Liver	Liver
30	chr6:128387400-128389600	Strong transcription	Fetal Stomach	stomach
31	chr6:128387400-128389600	Strong transcription	Ovary	ovary
32	chr6:128387600-128389600	Strong transcription	Fetal Intestine Large	intestine
33	chr6:128387600-128389600	Strong transcription	HepG2	liver
34	chr6:128387600-128390200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:128388000-128389600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr6:128388000-128389600	Strong transcription	Fetal Intestine Small	intestine
37	chr6:128388200-128389200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:128388200-128389400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr6:128388200-128389600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr6:128388200-128389600	Strong transcription	NHEK	skin
41	chr6:128388200-128393200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:128388400-128389600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:128388400-128390600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr6:128388600-128389400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr6:128388600-128389400	Enhancers	Fetal Brain Female	brain
46	chr6:128388600-128389400	Weak transcription	Fetal Muscle Leg	muscle
47	chr6:128388600-128389600	Enhancers	Left Ventricle	heart
48	chr6:128388600-128391600	Weak transcription	Primary B cells from cord blood	blood
49	chr6:128388600-128398200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:128388600-128398200	Weak transcription	HMEC	breast

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