Variant report

Variant	rs223317
Chromosome Location	chr4:103802824-103802825
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103746824..103748536-chr4:103800625..103803616,3	K562	blood:
2	chr4:103802810..103805581-chr4:103812817..103815542,2	K562	blood:
3	chr4:103795111..103797897-chr4:103800185..103803002,2	K562	blood:
4	chr4:103801030..103803497-chr4:103805639..103808341,2	K562	blood:
5	chr4:103742789..103744562-chr4:103800486..103802879,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10006474	0.95[CEU][hapmap]
rs10516495	0.91[CEU][hapmap]
rs10516496	0.91[CEU][hapmap]
rs11946020	0.95[CEU][hapmap]
rs13150953	0.91[CEU][hapmap]
rs223331	1.00[CEU][hapmap]
rs223361	1.00[CEU][hapmap]
rs223374	1.00[CEU][hapmap]
rs223401	0.87[CEU][hapmap]
rs223413	1.00[CEU][hapmap]
rs223471	1.00[CEU][hapmap]
rs2866416	0.96[CEU][hapmap]
rs34475639	0.95[CEU][hapmap]
rs4699048	0.87[CEU][hapmap]
rs6816370	0.96[CEU][hapmap]
rs6843738	0.95[CEU][hapmap]
rs7665026	0.95[CEU][hapmap]

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	nsv594957	chr4:103728010-103870091	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	esv1802717	chr4:103765156-103870091	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv879683	chr4:103785051-103916717	Flanking Active TSS Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	esv1849799	chr4:103787351-103881772	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs223317	KRT8P46	cis	lung	GTEx
rs223317	MANBA	cis	multi-tissue	Pritchard
rs223317	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs223317	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223317	LRRC37A15P	cis	Thyroid	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103791200-103834800	Weak transcription	Ovary	ovary
2	chr4:103791400-103806400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:103791400-103806600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:103791400-103806800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:103791400-103818600	Weak transcription	HSMMtube	muscle
6	chr4:103792200-103811000	Weak transcription	Osteobl	bone
7	chr4:103792800-103811400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:103793200-103810200	Weak transcription	HSMM	muscle
9	chr4:103796000-103809400	Weak transcription	HUVEC	blood vessel
10	chr4:103796000-103810800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:103796400-103811000	Weak transcription	Left Ventricle	heart
12	chr4:103796400-103819800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:103796600-103804800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:103798000-103804400	Weak transcription	Fetal Heart	heart
15	chr4:103798600-103811000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:103798800-103803600	Weak transcription	K562	blood
17	chr4:103798800-103804400	Weak transcription	Aorta	Aorta
18	chr4:103798800-103811000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:103799000-103803600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:103799000-103804200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:103799000-103806200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:103799000-103806400	Weak transcription	Dnd41	blood
23	chr4:103799000-103808200	Weak transcription	A549	lung
24	chr4:103799000-103808400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:103799000-103809400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:103799000-103809400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:103799000-103809800	Weak transcription	Lung	lung
28	chr4:103799000-103810000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:103799000-103810400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:103799000-103810600	Weak transcription	HMEC	breast
31	chr4:103799000-103811000	Weak transcription	Primary T cells from cord blood	blood
32	chr4:103799000-103811400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:103799000-103812800	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:103799000-103816800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:103799000-103817000	Weak transcription	Fetal Stomach	stomach
36	chr4:103799200-103803200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:103799200-103803400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:103799200-103803600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr4:103799200-103803600	Weak transcription	GM12878-XiMat	blood
40	chr4:103799200-103804400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:103799200-103804400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:103799200-103810600	Weak transcription	Fetal Brain Female	brain
43	chr4:103799200-103811000	Weak transcription	Fetal Intestine Large	intestine
44	chr4:103799200-103812400	Weak transcription	Fetal Muscle Leg	muscle
45	chr4:103799200-103812400	Weak transcription	Fetal Thymus	thymus
46	chr4:103799200-103817200	Weak transcription	Brain Germinal Matrix	brain
47	chr4:103799200-103819400	Weak transcription	Thymus	Thymus
48	chr4:103799400-103803200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:103799400-103811000	Weak transcription	Primary B cells from cord blood	blood
50	chr4:103799600-103811200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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