Variant report

Variant	rs41279517
Chromosome Location	chr4:53729771-53729772
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	EP300	chr4:53729310-53731670	SK-N-SH	brain:	n/a	chr4:53730198-53730206
2	SIN3A	chr4:53726721-53729851	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3AK20	chr4:53729437-53729777	H1-hESC	embryonic stem cell:	n/a	n/a
4	MXI1	chr4:53726951-53732052	SK-N-SH	brain:	n/a	n/a
5	ZNF384	chr4:53729688-53730017	K562	blood:	n/a	n/a
6	CHD1	chr4:53729588-53730108	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53586938..53589965-chr4:53727574..53731676,3	MCF-7	breast:
2	chr4:53577401..53580169-chr4:53726393..53730142,5	MCF-7	breast:

Variant related genes	Relation type
RASL11B	TF binding region
ENSG00000226950	Chromatin interaction
ENSG00000248375	Chromatin interaction
ENSG00000264585	Chromatin interaction
ENSG00000212588	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17082074	0.84[ASN][1000 genomes]
rs17698672	0.81[EUR][1000 genomes]
rs3811781	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58577680	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554057	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817433	0.95[ASN][1000 genomes]
rs6818178	0.95[ASN][1000 genomes]
rs6833350	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6848200	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855240	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73814875	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73814883	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814886	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7655781	0.95[ASN][1000 genomes]
rs7670068	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7677726	0.90[EUR][1000 genomes]
rs7685816	0.92[ASN][1000 genomes]
rs7699960	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs881744	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3360858	chr4:53727420-53729968	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53727800-53730800	Active TSS	Aorta	Aorta
2	chr4:53727800-53731800	Active TSS	Fetal Kidney	kidney
3	chr4:53728000-53729800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:53728000-53730000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr4:53728000-53730000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:53728000-53730200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:53728000-53730400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:53728200-53729800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:53728200-53729800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:53728200-53729800	Active TSS	Fetal Heart	heart
11	chr4:53728600-53730200	Active TSS	Right Atrium	heart
12	chr4:53728800-53729800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
13	chr4:53728800-53729800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
14	chr4:53728800-53729800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
15	chr4:53728800-53729800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
16	chr4:53728800-53730000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
17	chr4:53728800-53730000	Flanking Active TSS	Fetal Brain Male	brain
18	chr4:53728800-53730000	Flanking Active TSS	Placenta	Placenta
19	chr4:53728800-53731000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
20	chr4:53728800-53738400	Weak transcription	Small Intestine	intestine
21	chr4:53729200-53730200	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
22	chr4:53729200-53731800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:53729200-53732000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
24	chr4:53729200-53734200	Weak transcription	Psoas Muscle	Psoas
25	chr4:53729200-53734400	Weak transcription	HSMMtube	muscle
26	chr4:53729200-53735200	Weak transcription	Colonic Mucosa	Colon
27	chr4:53729200-53751200	Weak transcription	GM12878-XiMat	blood
28	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
29	chr4:53729400-53729800	Flanking Active TSS	Ovary	ovary
30	chr4:53729400-53730000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:53729400-53730000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:53729400-53730000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:53729400-53730600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:53729400-53730600	Weak transcription	Gastric	stomach
35	chr4:53729400-53730800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:53729400-53731000	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:53729400-53731200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:53729400-53731400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:53729400-53731400	Weak transcription	Left Ventricle	heart
40	chr4:53729400-53731400	Weak transcription	Pancreas	Pancrea
41	chr4:53729400-53731400	Weak transcription	Right Ventricle	heart
42	chr4:53729400-53731600	Weak transcription	Lung	lung
43	chr4:53729400-53732000	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
44	chr4:53729400-53732200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
45	chr4:53729400-53734000	Weak transcription	Brain Anterior Caudate	brain
46	chr4:53729400-53738600	Weak transcription	HMEC	breast
47	chr4:53729400-53739200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:53729400-53743200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:53729400-53752400	Weak transcription	Primary B cells from cord blood	blood
50	chr4:53729400-53753800	Weak transcription	Duodenum Mucosa	Duodenum

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