Variant report

Variant	rs35279
Chromosome Location	chr5:58653150-58653151
allele	C/G
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	BCL3	chr5:58652380-58654882	A549	lung:	n/a	chr5:58654065-58654072
2	TCF7L2	chr5:58652992-58653952	HEK293	kidney:	n/a	n/a
3	FOSL2	chr5:58653148-58654100	A549	lung:	n/a	chr5:58653410-58653421 chr5:58653310-58653322
4	TCF12	chr5:58652080-58654909	A549	lung:	n/a	chr5:58654406-58654414
5	CEBPB	chr5:58652711-58653861	A549	lung:	n/a	chr5:58653463-58653476
6	EP300	chr5:58652125-58654870	A549	lung:	n/a	chr5:58654367-58654381 chr5:58654145-58654155 chr5:58652862-58652871
7	FOXA2	chr5:58652736-58653943	A549	lung:	n/a	n/a
8	SP1	chr5:58652536-58654758	A549	lung:	n/a	chr5:58654561-58654575
9	REST	chr5:58652550-58654735	A549	lung:	n/a	n/a
10	TCF12	chr5:58653090-58653951	A549	lung:	n/a	n/a
11	SP1	chr5:58652205-58654846	A549	lung:	n/a	chr5:58654561-58654575
12	MAX	chr5:58652471-58654025	A549	lung:	n/a	n/a
13	GATA3	chr5:58652110-58654936	A549	lung:	n/a	chr5:58652911-58652921 chr5:58654911-58654920 chr5:58652912-58652924 chr5:58654060-58654076 chr5:58652566-58652576 chr5:58654798-58654806 chr5:58652914-58652921
14	EP300	chr5:58652087-58654835	A549	lung:	n/a	chr5:58654367-58654381 chr5:58654145-58654155 chr5:58652862-58652871
15	ZNF263	chr5:58652408-58654786	HEK293-T-REx	kidney:	n/a	chr5:58654513-58654522
16	ATF3	chr5:58652777-58654067	A549	lung:	n/a	n/a
17	CEBPB	chr5:58652378-58654781	A549	lung:	n/a	chr5:58654387-58654404 chr5:58653463-58653476
18	KAP1	chr5:58652373-58654510	U2OS	brain:	n/a	n/a
19	MAX	chr5:58652118-58654843	A549	lung:	n/a	chr5:58652436-58652445
20	JUND	chr5:58653145-58654002	A549	lung:	n/a	chr5:58653410-58653421 chr5:58653310-58653322
21	SIN3AK20	chr5:58653117-58653932	A549	lung:	n/a	n/a
22	SIX5	chr5:58652647-58654748	A549	lung:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs154024	0.92[EUR][1000 genomes]
rs154031	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs168641	0.93[ASN][1000 genomes]
rs2441091	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs244573	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs244574	0.83[AFR][1000 genomes]
rs244577	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs244579	0.87[AFR][1000 genomes]
rs244580	0.81[AFR][1000 genomes]
rs244582	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs244583	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs244586	0.88[ASN][1000 genomes]
rs244588	0.90[ASN][1000 genomes]
rs35258	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35261	0.91[EUR][1000 genomes]
rs35267	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35274	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35276	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35277	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35278	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35283	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35284	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs39672	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40122	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40126	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs40328	0.86[AFR][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	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1032732	chr5:58637179-58689010	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1022160	chr5:58645805-58689010	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58642200-58653200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:58646200-58654400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58648000-58654200	Weak transcription	Ovary	ovary
4	chr5:58648600-58653400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:58648600-58653800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:58649400-58653600	Weak transcription	Brain Anterior Caudate	brain
7	chr5:58649400-58653600	Weak transcription	Brain Substantia Nigra	brain
8	chr5:58649400-58654000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:58649400-58654200	Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr5:58649600-58653600	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr5:58651400-58653200	Active TSS	Primary B cells from cord blood	blood
12	chr5:58652000-58653400	Flanking Active TSS	A549	lung
13	chr5:58652000-58654400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:58652200-58653200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr5:58652200-58653400	Enhancers	Primary hematopoietic stem cells	blood
16	chr5:58652200-58653600	Enhancers	Rectal Smooth Muscle	rectum
17	chr5:58652200-58654400	Enhancers	Fetal Lung	lung
18	chr5:58652200-58654800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr5:58652200-58654800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr5:58652200-58655000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:58652200-58655000	Enhancers	Fetal Intestine Small	intestine
22	chr5:58652200-58656200	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr5:58652200-58656600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr5:58652400-58653200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr5:58652400-58653400	Enhancers	Colon Smooth Muscle	Colon
26	chr5:58652400-58653800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr5:58652400-58653800	Enhancers	Primary T cells from cord blood	blood
28	chr5:58652400-58654400	Enhancers	Fetal Intestine Large	intestine
29	chr5:58652400-58654800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr5:58652400-58655000	Enhancers	Stomach Mucosa	stomach
31	chr5:58652400-58655200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:58652400-58655200	Enhancers	Fetal Kidney	kidney
33	chr5:58652400-58655800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:58652400-58656400	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr5:58652600-58653200	Enhancers	Small Intestine	intestine
36	chr5:58652600-58653800	Enhancers	Placenta	Placenta
37	chr5:58652600-58654200	Enhancers	Brain Angular Gyrus	brain
38	chr5:58652600-58654600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:58652600-58654600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:58652600-58654600	Enhancers	Fetal Muscle Leg	muscle
41	chr5:58652600-58654600	Enhancers	Fetal Stomach	stomach
42	chr5:58652600-58654600	Enhancers	Fetal Thymus	thymus
43	chr5:58652600-58654600	Enhancers	Pancreas	Pancrea
44	chr5:58652600-58654800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr5:58652600-58654800	Enhancers	Gastric	stomach
46	chr5:58652600-58654800	Enhancers	Placenta Amnion	Placenta Amnion
47	chr5:58652600-58655000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:58652600-58655000	Enhancers	Brain Hippocampus Middle	brain
49	chr5:58652600-58655000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr5:58652600-58655200	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links