Variant report

Variant	rs223397
Chromosome Location	chr4:103742651-103742652
allele	C/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	chr4:103741330..103752134-chr4:103778393..103796398,92	K562	blood:

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

Extended variants
information (count: 108 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10003326	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10012413	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10015289	0.90[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs11097796	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs11722779	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11731885	0.90[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs11737544	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12500379	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs12508069	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs13150426	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1383733	0.89[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs150893	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs150895	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs17033015	0.80[YRI][hapmap]
rs17033381	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2086499	0.91[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs223308	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223313	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs223314	0.95[CEU][hapmap]
rs223315	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs223318	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223324	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs223326	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223330	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223334	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs223338	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223339	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs223346	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223349	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223350	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs223353	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs223356	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223358	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223359	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223363	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs223367	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223381	0.96[CEU][hapmap]
rs223383	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs223385	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223390	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223392	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223395	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs223400	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223401	0.91[JPT][hapmap]
rs223410	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs223412	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs223418	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs223419	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223420	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs223425	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223438	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs223441	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223447	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs223448	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223450	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223452	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs223454	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs223457	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs223458	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs223461	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223467	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs223474	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223475	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223484	0.90[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs223486	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs223497	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs223498	0.89[ASW][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs227368	1.00[YRI][hapmap]
rs227375	1.00[YRI][hapmap]
rs28445579	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs2866417	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3774987	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3886722	0.89[CEU][hapmap]
rs3886723	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs3974485	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3974604	0.90[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs3974608	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4623004	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs4698874	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs5028609	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6419160	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs6533041	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533050	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs6533051	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533052	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs65671	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs6810668	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs6815526	0.89[ASW][hapmap]
rs6823625	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs6824070	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6842179	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6846762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6852141	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6853193	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs724447	0.90[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs7254	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7663876	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7672319	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7676765	0.90[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs7676943	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7681629	0.90[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs7685399	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs7698608	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9307281	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs9999303	0.90[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][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
rs223397	CISD2	cis	Esophagus Muscularis	GTEx
rs223397	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223397	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223397	CISD2	cis	multi-tissue	Pritchard
rs223397	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs223397	KRT8P46	cis	lung	GTEx
rs223397	LRRC37A15P	cis	lung	GTEx
rs223397	CISD2	cis	Nerve Tibial	GTEx
rs223397	MANBA	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103713000-103744400	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	chr4:103733400-103743200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:103734600-103745600	Weak transcription	Fetal Stomach	stomach
11	chr4:103734800-103744800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:103735600-103746200	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr4:103736000-103746600	Weak transcription	Pancreas	Pancrea
14	chr4:103736600-103744400	Genic enhancers	HSMM	muscle
15	chr4:103736800-103743600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
16	chr4:103737200-103742800	Genic enhancers	Dnd41	blood
17	chr4:103737200-103745600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr4:103737400-103744800	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr4:103737600-103744200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:103737600-103744400	Enhancers	Colon Smooth Muscle	Colon
21	chr4:103737800-103743200	Enhancers	Adipose Nuclei	Adipose
22	chr4:103738000-103744200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:103738000-103744600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr4:103738400-103743200	Weak transcription	Spleen	Spleen
25	chr4:103738400-103743600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr4:103738400-103746600	Weak transcription	Gastric	stomach
27	chr4:103739000-103744400	Enhancers	Brain Anterior Caudate	brain
28	chr4:103739400-103744200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
29	chr4:103739400-103744200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr4:103739400-103744800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:103739400-103745600	Weak transcription	Placenta	Placenta
32	chr4:103739600-103742800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
33	chr4:103739600-103743200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr4:103739600-103744200	Enhancers	Rectal Smooth Muscle	rectum
35	chr4:103739600-103744400	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:103739800-103743200	Weak transcription	Hela-S3	cervix
37	chr4:103740200-103743400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:103740200-103743400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:103740200-103743800	Strong transcription	Fetal Thymus	thymus
40	chr4:103740200-103744600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:103740200-103744600	Enhancers	Brain Cingulate Gyrus	brain
42	chr4:103740200-103745600	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr4:103740400-103743800	Active TSS	Psoas Muscle	Psoas
44	chr4:103740400-103746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:103740600-103742800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr4:103740600-103743200	Enhancers	Brain Hippocampus Middle	brain
47	chr4:103740600-103743400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:103740600-103743600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:103740600-103744000	Genic enhancers	NH-A	brain
50	chr4:103740600-103744400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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