Variant report

Variant	rs223346
Chromosome Location	chr4:103780496-103780497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103741330..103752134-chr4:103778393..103796398,92	K562	blood:
2	chr4:103736995..103756245-chr4:103778393..103800311,117	K562	blood:

Variant related genes	Relation type
ENSG00000246560	Chromatin interaction
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10003326	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10012413	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10015289	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1080081	0.85[CHB][hapmap]
rs11097796	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11722779	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11731885	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11737544	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs12500379	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs12508069	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs13130741	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs13150426	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1383733	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs150893	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs150895	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17033381	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs2086499	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs223308	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223313	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs223315	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223318	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223326	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223330	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs223338	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223339	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs223349	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223350	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs223353	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223356	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223358	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223359	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223363	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223367	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223383	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223385	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs223390	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223392	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223395	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223397	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223400	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223401	0.91[JPT][hapmap]
rs223410	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223412	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223418	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223419	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223420	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223441	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223446	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223447	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223448	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223450	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223452	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223454	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223457	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223458	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223461	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs223467	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs223474	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223475	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223484	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223486	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs223497	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs28445579	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2866417	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs3774987	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3886723	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3974485	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs3974604	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3974608	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs4623004	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs4698874	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs4699049	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs5028609	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6419160	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6533041	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533050	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533051	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533052	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs65671	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6810668	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6823625	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6824070	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6842179	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs6846762	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6852141	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6853193	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs724447	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7254	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7660298	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7663876	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7672319	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7676765	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7676943	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7681629	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7685399	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7694724	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7698608	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs9307281	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs9999303	0.95[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv10541	chr4:103778446-103785639	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv3467281	chr4:103778813-103781269	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3467282	chr4:103778813-103781269	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv21280	chr4:103779278-103783640	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv594958	chr4:103780496-103782321	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv594959	chr4:103780496-103782582	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv594960	chr4:103780496-103782764	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv594961	chr4:103780496-103783359	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv594962	chr4:103780496-103783412	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs223346	CISD2	cis	Nerve Tibial	GTEx
rs223346	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223346	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223346	KRT8P46	cis	lung	GTEx
rs223346	CISD2	cis	multi-tissue	Pritchard
rs223346	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs223346	CISD2	cis	lung	GTEx
rs223346	MANBA	cis	multi-tissue	Pritchard

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103750800-103788000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:103765000-103783600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:103765400-103788800	Weak transcription	Left Ventricle	heart
4	chr4:103768600-103781800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:103779000-103787600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:103780000-103781000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:103780000-103781000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:103780000-103782000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr4:103780000-103788000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:103780200-103780800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
11	chr4:103780200-103782200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:103780200-103782800	ZNF genes & repeats	Dnd41	blood
13	chr4:103780200-103789200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:103780400-103781000	ZNF genes & repeats	Primary T cells from cord blood	blood
15	chr4:103780400-103788800	Weak transcription	Muscle Satellite Cultured Cells	--

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