Variant report

Variant	rs223497
Chromosome Location	chr4:103653976-103653977
allele	C/T
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	GATA3	chr4:103653327-103654084	MCF-7	breast:	n/a	chr4:103653464-103653475
2	GATA3	chr4:103653452-103653982	MCF-7	breast:	n/a	chr4:103653464-103653475
3	SIN3AK20	chr4:103653334-103654174	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103651533..103654531-chr4:103655303..103657953,2	K562	blood:

Variant related genes	Relation type
LRRC37A15P	TF binding region
KRT8P46	TF binding region
ENSG00000224207	TF binding region
ENSG00000224207	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10012413	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs11722779	0.85[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap]
rs150893	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs150895	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223308	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223313	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs223314	0.87[CEU][hapmap]
rs223315	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223318	0.83[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs223324	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223326	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223330	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs223334	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223338	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs223339	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223346	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223347	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223349	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs223350	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs223353	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223356	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs223358	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs223359	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223363	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223367	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223381	0.89[CEU][hapmap]
rs223383	0.84[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs223385	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223390	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223392	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs223395	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs223397	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs223400	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs223401	0.81[JPT][hapmap]
rs223410	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223412	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223418	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs223419	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs223420	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223425	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs223438	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223441	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223446	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223447	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223448	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223450	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs223452	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223454	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223457	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223458	0.89[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223461	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs223467	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223474	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs223475	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs223484	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs223486	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223498	0.89[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs227368	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs227375	0.84[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs3774987	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs3974604	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3974608	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs65671	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs6823625	0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs6824070	0.85[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap]
rs6846762	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs7254	0.85[CEU][hapmap];0.96[CHB][hapmap];0.86[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	nsv1008110	chr4:103560583-103684526	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs223497	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs223497	KRT8P46	cis	lung	GTEx
rs223497	MANBA	cis	multi-tissue	Pritchard
rs223497	CISD2	cis	Nerve Tibial	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
2	chr4:103571800-103655800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:103581800-103681000	Weak transcription	Spleen	Spleen
4	chr4:103609600-103664800	Weak transcription	Esophagus	oesophagus
5	chr4:103618400-103655800	Weak transcription	HSMM	muscle
6	chr4:103627400-103655400	Weak transcription	Lung	lung
7	chr4:103630400-103655800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:103632400-103666200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:103632400-103667600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:103634400-103655400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:103634600-103655400	Weak transcription	NHDF-Ad	bronchial
12	chr4:103634600-103655600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:103634600-103655600	Weak transcription	NHLF	lung
14	chr4:103634800-103655800	Weak transcription	Osteobl	bone
15	chr4:103637000-103680800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:103638800-103681000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:103639000-103656000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:103639200-103659400	Weak transcription	Ovary	ovary
19	chr4:103639600-103655800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:103641000-103671600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr4:103641200-103656200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:103641200-103680800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:103641400-103657800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:103641400-103659400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:103644400-103655400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr4:103644600-103658200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:103644800-103655600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:103644800-103658000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:103644800-103658000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:103645000-103655200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:103645400-103657200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:103645400-103658200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:103647600-103670400	Weak transcription	Liver	Liver
34	chr4:103648800-103655800	Weak transcription	Right Atrium	heart
35	chr4:103650200-103658200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr4:103651000-103654800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:103651000-103681000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:103651200-103656200	Weak transcription	Fetal Intestine Large	intestine
39	chr4:103651400-103654000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
40	chr4:103651400-103654200	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr4:103651400-103655800	Weak transcription	Pancreas	Pancrea
42	chr4:103651400-103656000	Weak transcription	Thymus	Thymus
43	chr4:103651800-103654000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
44	chr4:103651800-103655400	Weak transcription	Right Ventricle	heart
45	chr4:103652000-103678800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:103652200-103655200	Weak transcription	HepG2	liver
47	chr4:103652400-103655000	Weak transcription	K562	blood
48	chr4:103652400-103658800	Weak transcription	Fetal Stomach	stomach
49	chr4:103652400-103665800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:103652600-103655800	Weak transcription	Placenta	Placenta

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