Variant report

Variant	rs2005451
Chromosome Location	chr4:2853622-2853623
allele	G/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	RUNX3	chr4:2852934-2853759	GM12878	blood:	n/a	chr4:2853314-2853323 chr4:2853314-2853323
2	RUNX3	chr4:2852875-2853779	GM12878	blood:	n/a	chr4:2853314-2853323 chr4:2853314-2853323
3	PAX5	chr4:2853600-2853772	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2843889..2847586-chr4:2849028..2855037,6	K562	blood:
2	chr4:2819892..2821779-chr4:2853270..2855073,2	MCF-7	breast:
3	chr4:2845095..2847586-chr4:2852811..2854373,2	K562	blood:

Variant related genes	Relation type
ADD1	TF binding region
ENSG00000087266	Chromatin interaction
ENSG00000087274	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	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1263331	1.00[ASN][1000 genomes]
rs1574473	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843169	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843481	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843500	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843535	0.89[AFR][1000 genomes];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]
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	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];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	0.84[AFR][1000 genomes];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	1.00[AFR][1000 genomes];1.00[AMR][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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58928665	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59426248	0.95[AFR][1000 genomes];1.00[AMR][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	1.00[AFR][1000 genomes];1.00[AMR][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	chr4:2846800-2854200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:2846800-2855400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:2846800-2855400	Weak transcription	Placenta	Placenta
6	chr4:2846800-2855600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:2846800-2857400	Weak transcription	Aorta	Aorta
8	chr4:2846800-2861800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:2846800-2861800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:2846800-2862000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:2846800-2862600	Weak transcription	Esophagus	oesophagus
12	chr4:2847200-2862200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:2847400-2854400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr4:2847400-2854400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr4:2847400-2859800	Weak transcription	A549	lung
16	chr4:2847400-2863600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:2847800-2854200	Enhancers	Primary B cells from peripheral blood	blood
18	chr4:2847800-2854200	Weak transcription	NH-A	brain
19	chr4:2847800-2854200	Weak transcription	Osteobl	bone
20	chr4:2847800-2854600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:2847800-2854800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:2847800-2855400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:2847800-2856200	Weak transcription	HMEC	breast
24	chr4:2848000-2854200	Weak transcription	HUVEC	blood vessel
25	chr4:2848000-2854400	Weak transcription	NHEK	skin
26	chr4:2848000-2855400	Weak transcription	Fetal Stomach	stomach
27	chr4:2848000-2861200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:2848200-2854200	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr4:2848200-2854200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr4:2848400-2855400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:2849200-2854200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:2849200-2854200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr4:2849200-2854400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr4:2849200-2854800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr4:2849200-2855400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:2849200-2855400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:2849400-2854200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr4:2849400-2855400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr4:2849600-2854400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr4:2849600-2854600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:2850000-2860400	Weak transcription	Fetal Brain Male	brain
42	chr4:2850400-2855600	Enhancers	Primary hematopoietic stem cells	blood
43	chr4:2850400-2856400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:2851000-2860000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr4:2851200-2855400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr4:2851200-2856000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr4:2851400-2854000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:2851400-2854400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:2851400-2854400	Weak transcription	Colonic Mucosa	Colon
50	chr4:2851400-2857400	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links