Variant report

Variant	rs223400
Chromosome Location	chr4:103741596-103741597
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103680657..103683210-chr4:103740913..103743841,3	MCF-7	breast:
2	chr4:103740711..103743615-chr4:103789867..103792849,2	MCF-7	breast:
3	chr4:103736995..103756245-chr4:103778393..103800311,117	K562	blood:
4	chr4:103713070..103714725-chr4:103740099..103742111,2	K562	blood:
5	chr4:103741330..103752134-chr4:103778393..103796398,92	K562	blood:

Variant related genes	Relation type
ENSG00000145354	Chromatin interaction
ENSG00000238948	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000109323	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10003326	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs10012413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10015289	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs11097796	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11722779	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs11731885	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11737544	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12500379	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs12508069	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs13150426	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1383733	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs150893	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs150895	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17033381	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs2086499	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs223308	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223313	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs223314	1.00[CEU][hapmap]
rs223315	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223318	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs223330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223334	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223338	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223339	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223346	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs223350	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs223353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs223358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223359	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223363	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223367	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223381	1.00[CEU][hapmap]
rs223383	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223385	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223395	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223397	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223401	0.91[JPT][hapmap]
rs223410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223412	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs223420	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs223438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223441	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs223447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223448	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs223452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223454	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223457	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs223461	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223467	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223474	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs223475	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs223484	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223486	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223497	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs28445579	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2866417	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3774987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs3886722	0.93[CEU][hapmap]
rs3886723	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3974485	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3974604	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs3974608	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4623004	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4698874	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs5028609	0.93[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs6419160	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533041	0.93[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs6533050	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533051	0.92[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs6533052	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs65671	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6810668	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6815526	0.84[YRI][hapmap]
rs6823625	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6824070	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs6842179	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6846762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs6852141	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs6853193	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs724447	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7254	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs7663876	0.93[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs7672319	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7676765	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7676943	0.93[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap]
rs7681629	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7685399	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs7698608	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs9307281	0.96[CHB][hapmap];0.91[JPT][hapmap]
rs9999303	0.96[CEU][hapmap];0.95[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	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs223400	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs223400	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223400	LRRC37A15P	cis	lung	GTEx
rs223400	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223400	CISD2	cis	Nerve Tibial	GTEx
rs223400	MANBA	cis	multi-tissue	Pritchard
rs223400	KRT8P46	cis	lung	GTEx
rs223400	CISD2	cis	multi-tissue	Pritchard
rs223400	CISD2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103713000-103744400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:103724400-103745800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:103725600-103745000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:103728400-103744400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:103732600-103744400	Weak transcription	Brain Germinal Matrix	brain
6	chr4:103732800-103745000	Weak transcription	Lung	lung
7	chr4:103732800-103746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:103732800-103746400	Weak transcription	Esophagus	oesophagus
9	chr4:103733000-103741600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:103733400-103743200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:103734600-103745600	Weak transcription	Fetal Stomach	stomach
12	chr4:103734800-103744800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:103735600-103746200	Genic enhancers	Primary B cells from peripheral blood	blood
14	chr4:103735800-103741800	Enhancers	Small Intestine	intestine
15	chr4:103736000-103746600	Weak transcription	Pancreas	Pancrea
16	chr4:103736600-103742200	Enhancers	Brain Angular Gyrus	brain
17	chr4:103736600-103744400	Genic enhancers	HSMM	muscle
18	chr4:103736800-103743600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
19	chr4:103737200-103742000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
20	chr4:103737200-103742200	Genic enhancers	A549	lung
21	chr4:103737200-103742800	Genic enhancers	Dnd41	blood
22	chr4:103737200-103745600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr4:103737400-103744800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr4:103737600-103742200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:103737600-103744200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:103737600-103744400	Enhancers	Colon Smooth Muscle	Colon
27	chr4:103737800-103743200	Enhancers	Adipose Nuclei	Adipose
28	chr4:103738000-103744200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:103738000-103744600	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr4:103738400-103741600	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr4:103738400-103743200	Weak transcription	Spleen	Spleen
32	chr4:103738400-103743600	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr4:103738400-103746600	Weak transcription	Gastric	stomach
34	chr4:103738800-103742400	Genic enhancers	Osteobl	bone
35	chr4:103739000-103742000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:103739000-103744400	Enhancers	Brain Anterior Caudate	brain
37	chr4:103739200-103742000	Enhancers	Stomach Mucosa	stomach
38	chr4:103739400-103742400	Enhancers	NHLF	lung
39	chr4:103739400-103744200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
40	chr4:103739400-103744200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr4:103739400-103744800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:103739400-103745600	Weak transcription	Placenta	Placenta
43	chr4:103739600-103741800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:103739600-103742800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
45	chr4:103739600-103743200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr4:103739600-103744200	Enhancers	Rectal Smooth Muscle	rectum
47	chr4:103739600-103744400	Weak transcription	Fetal Muscle Leg	muscle
48	chr4:103739800-103741600	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr4:103739800-103742000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr4:103739800-103742400	Enhancers	Fetal Intestine Large	intestine

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