Variant report

Variant	rs223392
Chromosome Location	chr4:103745756-103745757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr4:103745619-103745825	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:103745493-103745926	U87	brain:	n/a	n/a
3	MXI1	chr4:103745018-103750658	IMR90	lung:	n/a	n/a
4	POLR2A	chr4:103744252-103750750	K562	blood:	n/a	n/a
5	MXI1	chr4:103744961-103750789	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr4:103745375-103745824	MCF10A-Er-Src	breast:	n/a	n/a
7	CHD1	chr4:103743990-103750660	IMR90	lung:	n/a	chr4:103748391-103748401 chr4:103748142-103748152 chr4:103747370-103747377
8	MYC	chr4:103745312-103746039	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr4:103745668-103745974	A549	lung:	n/a	n/a
10	GATA3	chr4:103745535-103745925	SH-SY5Y	brain:	n/a	n/a
11	POLR2A	chr4:103744603-103746075	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:103745741-103745786	HepG2	liver:	n/a	n/a
13	CHD1	chr4:103745496-103750418	H1-hESC	embryonic stem cell:	n/a	chr4:103748391-103748401 chr4:103748142-103748152 chr4:103747370-103747377
14	POLR2A	chr4:103745091-103745769	GM12878	blood:	n/a	n/a
15	IRF1	chr4:103745748-103747544	K562	blood:	n/a	chr4:103746101-103746115
16	CHD1	chr4:103745634-103745936	GM12878	blood:	n/a	n/a
17	POLR2A	chr4:103745586-103746094	GM12892	blood:	n/a	n/a
18	POLR2A	chr4:103745228-103745999	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103744455..103746135-chr4:103804682..103806272,2	K562	blood:
2	chr4:103680756..103682755-chr4:103744966..103746482,2	MCF-7	breast:
3	chr4:103680426..103684137-chr4:103744957..103747230,3	K562	blood:
4	chr4:103721670..103724216-chr4:103745688..103748268,3	MCF-7	breast:
5	chr4:103745482..103752084-chr4:103788371..103792114,20	MCF-7	breast:
6	chr4:103736995..103756245-chr4:103778393..103800311,117	K562	blood:
7	chr4:103422194..103424603-chr4:103745115..103749014,4	K562	blood:
8	chr4:103741330..103752134-chr4:103778393..103796398,92	K562	blood:

Variant related genes	Relation type
ENSG00000246560	TF binding region
ENSG00000145354	Chromatin interaction
ENSG00000260651	Chromatin interaction
ENSG00000109320	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000238948	Chromatin interaction
ENSG00000109323	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10003326	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs10012413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10015289	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][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]
rs11731885	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11737544	0.93[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs12500379	0.96[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap]
rs12508069	0.96[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap]
rs13150426	0.93[CEU][hapmap];0.87[CHB][hapmap];0.91[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];0.87[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]
rs223326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
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]
rs223350	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs223353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
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]
rs223400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223401	0.95[JPT][hapmap]
rs223410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs223420	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs223447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs223452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
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]
rs223475	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223484	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][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];0.87[JPT][hapmap]
rs3774987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.87[JPT][hapmap]
rs3974604	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][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]
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]
rs6842179	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs6846762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6852141	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs6853193	0.96[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap]
rs724447	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7254	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.86[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
rs223392	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs223392	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223392	KRT8P46	cis	lung	GTEx
rs223392	MANBA	cis	multi-tissue	Pritchard
rs223392	CISD2	cis	multi-tissue	Pritchard
rs223392	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223392	CISD2	cis	Nerve Tibial	GTEx
rs223392	CISD2	cis	Esophagus Muscularis	GTEx
rs223392	LRRC37A15P	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103724400-103745800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:103732800-103746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:103732800-103746400	Weak transcription	Esophagus	oesophagus
4	chr4:103735600-103746200	Genic enhancers	Primary B cells from peripheral blood	blood
5	chr4:103736000-103746600	Weak transcription	Pancreas	Pancrea
6	chr4:103738400-103746600	Weak transcription	Gastric	stomach
7	chr4:103740400-103746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:103740800-103747200	Transcr. at gene 5' and 3'	K562	blood
9	chr4:103741200-103745800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:103742000-103750200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr4:103742600-103745800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:103742600-103748400	Active TSS	Right Atrium	heart
13	chr4:103742800-103747800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:103742800-103748000	Transcr. at gene 5' and 3'	Dnd41	blood
15	chr4:103742800-103748800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:103743200-103745800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
17	chr4:103743200-103747200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr4:103743200-103750000	Active TSS	Aorta	Aorta
19	chr4:103743400-103746000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:103743400-103748200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:103743600-103745800	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr4:103743600-103750200	Active TSS	NHLF	lung
23	chr4:103743800-103745800	Enhancers	Spleen	Spleen
24	chr4:103744000-103745800	Transcr. at gene 5' and 3'	NH-A	brain
25	chr4:103744000-103746000	Transcr. at gene 5' and 3'	NHEK	skin
26	chr4:103744000-103747400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
27	chr4:103744000-103750400	Active TSS	Right Ventricle	heart
28	chr4:103744200-103745800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:103744200-103746000	Flanking Active TSS	Liver	Liver
30	chr4:103744200-103746000	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr4:103744200-103746000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr4:103744200-103746200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
33	chr4:103744200-103746400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
34	chr4:103744200-103746600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:103744200-103747000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
36	chr4:103744200-103747800	Transcr. at gene 5' and 3'	Osteobl	bone
37	chr4:103744200-103748200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
38	chr4:103744200-103748800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:103744200-103749600	Active TSS	Primary T cells fromperipheralblood	blood
40	chr4:103744400-103746000	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:103744400-103746000	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr4:103744400-103746000	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr4:103744400-103746000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr4:103744400-103746000	Transcr. at gene 5' and 3'	HepG2	liver
45	chr4:103744400-103746600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
46	chr4:103744400-103746600	Transcr. at gene 5' and 3'	HSMM	muscle
47	chr4:103744400-103746800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:103744400-103747800	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:103744400-103748600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
50	chr4:103744400-103750000	Active TSS	Ovary	ovary

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