Variant report

Variant	rs223395
Chromosome Location	chr4:103744958-103744959
allele	A/C
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	TBL1XR1	chr4:103744538-103745293	K562	blood:	n/a	n/a
2	POLR2A	chr4:103744252-103750750	K562	blood:	n/a	n/a
3	CHD1	chr4:103743990-103750660	IMR90	lung:	n/a	chr4:103748391-103748401 chr4:103748142-103748152 chr4:103747370-103747377
4	POLR2A	chr4:103744603-103746075	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:103744910-103745372	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103744455..103746135-chr4:103804682..103806272,2	K562	blood:
2	chr4:103709698..103712362-chr4:103742984..103745016,2	K562	blood:
3	chr4:103680426..103684137-chr4:103744957..103747230,3	K562	blood:
4	chr4:103736995..103756245-chr4:103778393..103800311,117	K562	blood:
5	chr4:103741330..103752134-chr4:103778393..103796398,92	K562	blood:

Variant related genes	Relation type
ENSG00000246560	TF binding region
ENSG00000145354	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000109323	Chromatin interaction
ENSG00000238948	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	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs10012413	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs10015289	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs11097796	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs11722779	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs11731885	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[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]
rs13150426	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs1383733	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs150893	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs150895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs17033381	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs2086499	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs223308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[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];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs223318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs223324	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223326	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223330	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223334	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223338	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs223346	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223347	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223349	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223350	0.96[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap]
rs223353	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223356	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223358	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs223363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs223367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs223381	0.96[CEU][hapmap]
rs223383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap]
rs223385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs223390	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223392	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223397	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223400	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223401	0.86[JPT][hapmap]
rs223410	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223412	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223418	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs223419	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223420	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs223425	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223438	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs223446	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223447	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs223450	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223452	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs223457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs223458	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs223467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs223474	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs223475	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs223484	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs223486	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223497	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs28445579	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2866417	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap]
rs3774987	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs3886722	0.96[CEU][hapmap];0.83[YRI][hapmap]
rs3886723	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs3974485	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs3974604	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3974608	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4623004	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4698874	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs5028609	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs6419160	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs6533041	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs6533050	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs6533051	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap]
rs6533052	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs65671	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6810668	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs6823625	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs6824070	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs6842179	0.93[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs6846762	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs6852141	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs6853193	0.93[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs724447	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7254	0.93[CEU][hapmap];0.96[CHB][hapmap];0.90[JPT][hapmap]
rs7663876	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs7672319	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7676765	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7676943	0.96[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs7681629	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7685399	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7698608	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9307281	0.92[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs9999303	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[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
rs223395	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223395	MANBA	cis	multi-tissue	Pritchard
rs223395	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs223395	LRRC37A15P	cis	lung	GTEx
rs223395	KRT8P46	cis	lung	GTEx
rs223395	CISD2	cis	Esophagus Muscularis	GTEx
rs223395	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223395	CISD2	cis	Nerve Tibial	GTEx
rs223395	CISD2	cis	multi-tissue	Pritchard

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	chr4:103725600-103745000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:103732800-103745000	Weak transcription	Lung	lung
4	chr4:103732800-103746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:103732800-103746400	Weak transcription	Esophagus	oesophagus
6	chr4:103734600-103745600	Weak transcription	Fetal Stomach	stomach
7	chr4:103735600-103746200	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr4:103736000-103746600	Weak transcription	Pancreas	Pancrea
9	chr4:103737200-103745600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr4:103738400-103746600	Weak transcription	Gastric	stomach
11	chr4:103739400-103745600	Weak transcription	Placenta	Placenta
12	chr4:103740200-103745600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr4:103740400-103746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:103740800-103747200	Transcr. at gene 5' and 3'	K562	blood
15	chr4:103741200-103745000	Enhancers	Fetal Heart	heart
16	chr4:103741200-103745800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:103742000-103750200	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:103742400-103745000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:103742600-103745000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr4:103742600-103745600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr4:103742600-103745800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:103742600-103748400	Active TSS	Right Atrium	heart
23	chr4:103742800-103747800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:103742800-103748000	Transcr. at gene 5' and 3'	Dnd41	blood
25	chr4:103742800-103748800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:103743200-103745000	Genic enhancers	Hela-S3	cervix
27	chr4:103743200-103745600	Enhancers	Small Intestine	intestine
28	chr4:103743200-103745800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
29	chr4:103743200-103747200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr4:103743200-103750000	Active TSS	Aorta	Aorta
31	chr4:103743400-103746000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:103743400-103748200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:103743600-103745800	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr4:103743600-103750200	Active TSS	NHLF	lung
35	chr4:103743800-103745600	Genic enhancers	Fetal Thymus	thymus
36	chr4:103743800-103745800	Enhancers	Spleen	Spleen
37	chr4:103744000-103745000	Active TSS	Stomach Smooth Muscle	stomach
38	chr4:103744000-103745200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr4:103744000-103745400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr4:103744000-103745600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:103744000-103745800	Transcr. at gene 5' and 3'	NH-A	brain
42	chr4:103744000-103746000	Transcr. at gene 5' and 3'	NHEK	skin
43	chr4:103744000-103747400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
44	chr4:103744000-103750400	Active TSS	Right Ventricle	heart
45	chr4:103744200-103745000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:103744200-103745000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:103744200-103745000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:103744200-103745200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr4:103744200-103745200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
50	chr4:103744200-103745200	Transcr. at gene 5' and 3'	HMEC	breast

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