Variant report

Variant	rs223359
Chromosome Location	chr4:103770579-103770580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103770498..103773178-chr4:103786218..103788263,2	K562	blood:
2	chr4:103770002..103772196-chr4:103773207..103775445,3	K562	blood:
3	chr4:103763663..103765375-chr4:103769517..103772269,2	K562	blood:
4	chr4:103748010..103751949-chr4:103768515..103772820,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246560	Chromatin interaction
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10003326	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs10012413	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs10015289	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs1080081	0.92[CEU][hapmap]
rs11097796	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11722779	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs11731885	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11737544	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs12500379	0.93[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap]
rs12508069	0.93[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap]
rs13130741	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs13150426	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs1383733	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs150893	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs150895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17033381	0.93[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2086499	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs223308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223313	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs223314	0.96[CEU][hapmap]
rs223315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223324	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223326	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223330	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223334	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs223338	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223346	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223347	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs223349	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223350	0.96[CHB][hapmap];0.96[JPT][hapmap];0.88[YRI][hapmap]
rs223353	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223356	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223358	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs223381	0.96[CEU][hapmap]
rs223383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap]
rs223385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs223390	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223392	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs223397	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223400	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223401	0.91[JPT][hapmap]
rs223410	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223412	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223418	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223419	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223420	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223425	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223438	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223446	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223447	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223450	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223452	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223458	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs223467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs223474	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223475	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223484	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223486	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223497	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs28445579	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs2866417	0.96[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap]
rs3774987	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs3886722	0.96[CEU][hapmap];0.87[YRI][hapmap]
rs3886723	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap]
rs3974485	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap]
rs3974604	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3974608	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap]
rs4623004	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs4698874	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs4699049	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs5028609	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs6419160	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs6533041	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap]
rs6533050	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6533051	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap]
rs6533052	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs65671	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6810668	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6823625	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs6824070	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs6842179	0.93[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap]
rs6846762	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs6852141	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs6853193	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs724447	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7254	0.93[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs7660298	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7663876	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs7672319	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7676765	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7676943	0.96[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap]
rs7681629	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7685399	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap]
rs7694724	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7698608	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs9307281	0.92[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap]
rs9999303	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs223359	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs223359	MANBA	cis	multi-tissue	Pritchard
rs223359	CISD2	cis	multi-tissue	Pritchard
rs223359	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223359	CISD2	cis	Nerve Tibial	GTEx
rs223359	CISD2	cis	Esophagus Muscularis	GTEx
rs223359	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223359	KRT8P46	cis	lung	GTEx
rs223359	LRRC37A15P	cis	lung	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103750000-103770600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:103750600-103771200	Weak transcription	Brain Angular Gyrus	brain
3	chr4:103750800-103771400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:103750800-103788000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:103751600-103780200	Weak transcription	Dnd41	blood
6	chr4:103753600-103776000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:103754000-103770800	Weak transcription	K562	blood
8	chr4:103758200-103771200	Weak transcription	A549	lung
9	chr4:103760200-103772200	Weak transcription	Primary T cells from cord blood	blood
10	chr4:103761600-103779800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:103763400-103771400	Weak transcription	Fetal Stomach	stomach
12	chr4:103765000-103783600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:103765200-103780000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:103765400-103788800	Weak transcription	Left Ventricle	heart
15	chr4:103768600-103781800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:103769200-103772000	Weak transcription	Fetal Thymus	thymus

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