Variant report

Variant	rs6533577
Chromosome Location	chr4:79209998-79209999
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10010879	0.92[AFR][1000 genomes]
rs10013117	0.97[AFR][1000 genomes]
rs10014848	0.89[AFR][1000 genomes]
rs1378236	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1378240	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1580106	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1840387	1.00[AMR][1000 genomes]
rs345504	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs345505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs345508	1.00[AMR][1000 genomes]
rs345509	1.00[AMR][1000 genomes]
rs345510	1.00[AMR][1000 genomes]
rs345512	1.00[AMR][1000 genomes]
rs345537	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs369056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs391945	1.00[AMR][1000 genomes]
rs395228	1.00[AMR][1000 genomes]
rs405843	1.00[AMR][1000 genomes]
rs448495	1.00[AMR][1000 genomes]
rs4859522	0.85[AFR][1000 genomes]
rs649887	1.00[AMR][1000 genomes]
rs6533550	0.82[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.83[AFR][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	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv818246	chr4:79184338-79221851	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6533577	FABP3	trans	lymphoblastoid	seeQTL
rs6533577	G0S2	trans	lymphoblastoid	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79169800-79213800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:79174800-79214400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:79187600-79214800	Weak transcription	Left Ventricle	heart
4	chr4:79187800-79210400	Weak transcription	Fetal Kidney	kidney
5	chr4:79188600-79218400	Weak transcription	Aorta	Aorta
6	chr4:79191400-79213600	Weak transcription	Psoas Muscle	Psoas
7	chr4:79192200-79213800	Weak transcription	Fetal Heart	heart
8	chr4:79198200-79214000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:79198400-79212400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:79198600-79215600	Weak transcription	Esophagus	oesophagus
11	chr4:79198600-79217600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:79198600-79220200	Weak transcription	Pancreas	Pancrea
13	chr4:79198600-79221000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:79198600-79241400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:79198800-79213800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:79200600-79213600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:79200600-79213800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:79203600-79211600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:79203800-79210600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:79203800-79211000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:79203800-79211400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:79204000-79217600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:79205600-79211600	Strong transcription	HepG2	liver
24	chr4:79206400-79215000	Weak transcription	Right Atrium	heart
25	chr4:79207600-79213800	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:79207800-79213600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:79208400-79220800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:79208400-79229200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:79208800-79211200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:79208800-79218200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:79208800-79236800	Weak transcription	Fetal Intestine Large	intestine
32	chr4:79209000-79211400	Weak transcription	Fetal Intestine Small	intestine
33	chr4:79209200-79210000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:79209200-79210600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:79209200-79210600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:79209200-79217600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:79209400-79210000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:79209400-79210200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:79209400-79210200	Enhancers	Osteobl	bone
40	chr4:79209800-79210200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:79209800-79210400	Enhancers	HSMMtube	muscle
42	chr4:79209800-79210400	Enhancers	NHDF-Ad	bronchial
43	chr4:79209800-79213600	Weak transcription	Fetal Lung	lung

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