Variant report

Variant	rs223441
Chromosome Location	chr4:103715385-103715386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103714894..103716784-chr4:103747226..103749102,2	MCF-7	breast:
2	chr4:103709195..103711005-chr4:103715001..103717258,3	K562	blood:
3	chr4:103700767..103702630-chr4:103715058..103716943,2	K562	blood:

Variant related genes	Relation type
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:89)

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]
rs11722779	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs11737544	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12500379	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs12508069	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][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];0.91[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];0.95[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]
rs223359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][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]
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]
rs2866417	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[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];0.91[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]
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]
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]
rs7254	0.93[CEU][hapmap];0.96[CHB][hapmap];0.95[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]
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]
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:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526256	chr4:103712589-103728010	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs223441	CISD2	cis	Esophagus Muscularis	GTEx
rs223441	CISD2	cis	lung	GTEx
rs223441	CISD2	cis	multi-tissue	Pritchard
rs223441	CISD2	cis	Nerve Tibial	GTEx
rs223441	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223441	KRT8P46	cis	lung	GTEx
rs223441	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs223441	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223441	MANBA	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103699400-103725000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:103700200-103716800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:103700400-103716200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:103700600-103716000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:103700600-103731600	Weak transcription	Pancreas	Pancrea
6	chr4:103701400-103718000	Weak transcription	Lung	lung
7	chr4:103702200-103716200	Weak transcription	NHEK	skin
8	chr4:103702200-103719000	Weak transcription	Small Intestine	intestine
9	chr4:103702800-103717000	Weak transcription	Fetal Brain Male	brain
10	chr4:103704800-103716000	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:103706400-103716200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:103706400-103719000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:103707800-103716000	Weak transcription	Psoas Muscle	Psoas
14	chr4:103707800-103724800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:103707800-103732200	Weak transcription	Right Ventricle	heart
16	chr4:103710400-103718800	Weak transcription	Thymus	Thymus
17	chr4:103710600-103717000	Weak transcription	Hela-S3	cervix
18	chr4:103710800-103719600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:103711000-103716000	Weak transcription	Placenta	Placenta
20	chr4:103711000-103716800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:103711000-103717800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:103711200-103716200	Weak transcription	Brain Anterior Caudate	brain
23	chr4:103711200-103716200	Weak transcription	Fetal Lung	lung
24	chr4:103711200-103717000	Weak transcription	Fetal Kidney	kidney
25	chr4:103711200-103724800	Weak transcription	Fetal Stomach	stomach
26	chr4:103711200-103731000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:103711200-103731600	Weak transcription	Spleen	Spleen
28	chr4:103711400-103715800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr4:103711400-103716000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr4:103711400-103716000	Weak transcription	Brain Substantia Nigra	brain
31	chr4:103711400-103732600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:103711600-103719000	Weak transcription	Brain Germinal Matrix	brain
33	chr4:103711800-103715800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:103711800-103716200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:103711800-103728400	Strong transcription	HSMM	muscle
36	chr4:103712000-103715600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr4:103712200-103719600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:103712400-103716200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:103712400-103718000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:103712400-103718800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:103712400-103718800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:103712400-103720200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:103712400-103720400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:103712400-103724600	Strong transcription	A549	lung
45	chr4:103712400-103726200	Strong transcription	HSMMtube	muscle
46	chr4:103712400-103726800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr4:103712400-103729200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr4:103712400-103730000	Strong transcription	Primary hematopoietic stem cells	blood
49	chr4:103712400-103735000	Strong transcription	K562	blood
50	chr4:103712400-103736200	Strong transcription	Fetal Intestine Large	intestine

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