Variant report

Variant	rs1574473
Chromosome Location	chr4:2854382-2854383
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	BHLHE40	chr4:2854302-2854432	GM12878	blood:	n/a	n/a
2	EBF1	chr4:2854094-2854629	GM12878	blood:	n/a	chr4:2854285-2854296 chr4:2854287-2854296
3	EP300	chr4:2854235-2854532	GM12878	blood:	n/a	chr4:2854411-2854420 chr4:2854264-2854278
4	PAX5	chr4:2854347-2854614	GM12878	blood:	n/a	n/a
5	RUNX3	chr4:2854145-2854602	GM12878	blood:	n/a	n/a
6	EBF1	chr4:2854085-2854452	GM12878	blood:	n/a	chr4:2854285-2854296 chr4:2854287-2854296
7	ZNF384	chr4:2854216-2854823	K562	blood:	n/a	n/a
8	NFIC	chr4:2854063-2854782	GM12878	blood:	n/a	n/a
9	MXI1	chr4:2854362-2854694	GM12878	blood:	n/a	n/a
10	ZNF384	chr4:2854075-2854891	GM12878	blood:	n/a	n/a
11	BCLAF1	chr4:2854049-2854538	GM12878	blood:	n/a	n/a
12	EBF1	chr4:2854111-2854491	GM12878	blood:	n/a	chr4:2854285-2854296 chr4:2854287-2854296

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2843889..2847586-chr4:2849028..2855037,6	K562	blood:
2	chr4:2819892..2821779-chr4:2853270..2855073,2	MCF-7	breast:

Variant related genes	Relation type
ADD1	TF binding region
ENSG00000087274	Chromatin interaction
ENSG00000087266	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1034400	1.00[ASN][1000 genomes]
rs10488838	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1263331	1.00[ASN][1000 genomes]
rs16843169	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843451	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843454	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843481	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843500	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843535	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843539	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843553	1.00[ASN][1000 genomes]
rs16843596	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005451	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857845	1.00[ASN][1000 genomes]
rs34120252	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34241425	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34550139	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34585460	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743278	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34745961	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34945392	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35445752	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35508581	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35893718	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35913891	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36038921	1.00[ASN][1000 genomes]
rs41528047	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4741	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4969	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56975682	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57155428	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57174035	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57557041	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57763208	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58059873	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58132256	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58196520	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58731679	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58758786	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58928665	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59426248	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59786983	1.00[ASN][1000 genomes]
rs59790260	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59798370	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60169711	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61117606	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61339714	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv521858	chr4:2846799-2881256	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS 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
9	nsv526059	chr4:2850142-2861090	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv524060	chr4:2850142-2881256	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2846600-2854400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:2846600-2862400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:2846800-2855400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:2846800-2855400	Weak transcription	Placenta	Placenta
5	chr4:2846800-2855600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:2846800-2857400	Weak transcription	Aorta	Aorta
7	chr4:2846800-2861800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:2846800-2861800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:2846800-2862000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:2846800-2862600	Weak transcription	Esophagus	oesophagus
11	chr4:2847200-2862200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:2847400-2854400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr4:2847400-2854400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr4:2847400-2859800	Weak transcription	A549	lung
15	chr4:2847400-2863600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:2847800-2854600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:2847800-2854800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:2847800-2855400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:2847800-2856200	Weak transcription	HMEC	breast
20	chr4:2848000-2854400	Weak transcription	NHEK	skin
21	chr4:2848000-2855400	Weak transcription	Fetal Stomach	stomach
22	chr4:2848000-2861200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:2848400-2855400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:2849200-2854400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr4:2849200-2854800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr4:2849200-2855400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:2849200-2855400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:2849400-2855400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr4:2849600-2854400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr4:2849600-2854600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:2850000-2860400	Weak transcription	Fetal Brain Male	brain
32	chr4:2850400-2855600	Enhancers	Primary hematopoietic stem cells	blood
33	chr4:2850400-2856400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:2851000-2860000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr4:2851200-2855400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr4:2851200-2856000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr4:2851400-2854400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:2851400-2854400	Weak transcription	Colonic Mucosa	Colon
39	chr4:2851400-2857400	Weak transcription	Pancreas	Pancrea
40	chr4:2851600-2854400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:2851600-2854400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:2851800-2854400	Weak transcription	Ovary	ovary
43	chr4:2852000-2854400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:2852000-2854400	Weak transcription	Fetal Intestine Large	intestine
45	chr4:2852000-2855000	Weak transcription	Fetal Brain Female	brain
46	chr4:2852000-2860200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:2852000-2865800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:2852200-2855400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:2852200-2855400	Weak transcription	Lung	lung
50	chr4:2852400-2854600	Enhancers	Primary T cells fromperipheralblood	blood

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