Variant report

Variant	rs6877927
Chromosome Location	chr5:58653917-58653918
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	BCL3	chr5:58653155-58654805	A549	lung:	n/a	chr5:58654065-58654072
2	BCL3	chr5:58652380-58654882	A549	lung:	n/a	chr5:58654065-58654072
3	TCF7L2	chr5:58652992-58653952	HEK293	kidney:	n/a	n/a
4	CEBPB	chr5:58653216-58653932	A549	lung:	n/a	chr5:58653463-58653476
5	FOSL2	chr5:58653148-58654100	A549	lung:	n/a	chr5:58653410-58653421 chr5:58653310-58653322
6	TCF12	chr5:58652080-58654909	A549	lung:	n/a	chr5:58654406-58654414
7	EP300	chr5:58652125-58654870	A549	lung:	n/a	chr5:58654367-58654381 chr5:58654145-58654155 chr5:58652862-58652871
8	FOXA2	chr5:58652736-58653943	A549	lung:	n/a	n/a
9	SP1	chr5:58652536-58654758	A549	lung:	n/a	chr5:58654561-58654575
10	REST	chr5:58652550-58654735	A549	lung:	n/a	n/a
11	GATA3	chr5:58653330-58653960	A549	lung:	n/a	n/a
12	TCF12	chr5:58653090-58653951	A549	lung:	n/a	n/a
13	SP1	chr5:58652205-58654846	A549	lung:	n/a	chr5:58654561-58654575
14	HA-E2F1	chr5:58653420-58654053	MCF-7	breast:	n/a	n/a
15	MAX	chr5:58652471-58654025	A549	lung:	n/a	n/a
16	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
17	EP300	chr5:58652087-58654835	A549	lung:	n/a	chr5:58654367-58654381 chr5:58654145-58654155 chr5:58652862-58652871
18	ZNF263	chr5:58652408-58654786	HEK293-T-REx	kidney:	n/a	chr5:58654513-58654522
19	ATF3	chr5:58652777-58654067	A549	lung:	n/a	n/a
20	CEBPB	chr5:58652378-58654781	A549	lung:	n/a	chr5:58654387-58654404 chr5:58653463-58653476
21	KAP1	chr5:58652373-58654510	U2OS	brain:	n/a	n/a
22	MAX	chr5:58652118-58654843	A549	lung:	n/a	chr5:58652436-58652445
23	NR3C1	chr5:58653161-58653972	A549	lung:	n/a	n/a
24	JUND	chr5:58653145-58654002	A549	lung:	n/a	chr5:58653410-58653421 chr5:58653310-58653322
25	SIN3AK20	chr5:58653117-58653932	A549	lung:	n/a	n/a
26	SIX5	chr5:58652647-58654748	A549	lung:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10471469	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10472105	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10472106	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12055306	0.82[CEU][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12697177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13153653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13176940	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs16889615	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1823066	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs1823067	0.93[ASN][1000 genomes]
rs1823068	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs2059175	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2547919	0.93[ASN][1000 genomes]
rs255812	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2591747	0.90[ASN][1000 genomes]
rs2702363	0.82[CHB][hapmap]
rs2702365	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs35288	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35289	1.00[CHB][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6450517	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7723695	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv881704	chr5:58653383-58675538	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58646200-58654400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:58648000-58654200	Weak transcription	Ovary	ovary
3	chr5:58649400-58654000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:58649400-58654200	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr5:58652000-58654400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:58652200-58654400	Enhancers	Fetal Lung	lung
7	chr5:58652200-58654800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr5:58652200-58654800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr5:58652200-58655000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:58652200-58655000	Enhancers	Fetal Intestine Small	intestine
11	chr5:58652200-58656200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr5:58652200-58656600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr5:58652400-58654400	Enhancers	Fetal Intestine Large	intestine
14	chr5:58652400-58654800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr5:58652400-58655000	Enhancers	Stomach Mucosa	stomach
16	chr5:58652400-58655200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:58652400-58655200	Enhancers	Fetal Kidney	kidney
18	chr5:58652400-58655800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:58652400-58656400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr5:58652600-58654200	Enhancers	Brain Angular Gyrus	brain
21	chr5:58652600-58654600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:58652600-58654600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:58652600-58654600	Enhancers	Fetal Muscle Leg	muscle
24	chr5:58652600-58654600	Enhancers	Fetal Stomach	stomach
25	chr5:58652600-58654600	Enhancers	Fetal Thymus	thymus
26	chr5:58652600-58654600	Enhancers	Pancreas	Pancrea
27	chr5:58652600-58654800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr5:58652600-58654800	Enhancers	Gastric	stomach
29	chr5:58652600-58654800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr5:58652600-58655000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:58652600-58655000	Enhancers	Brain Hippocampus Middle	brain
32	chr5:58652600-58655000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr5:58652600-58655200	Enhancers	Fetal Brain Male	brain
34	chr5:58652600-58655800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:58652800-58654600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:58652800-58654600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:58652800-58656400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr5:58653000-58654000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr5:58653000-58654200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:58653000-58654400	Weak transcription	Left Ventricle	heart
41	chr5:58653000-58654600	Enhancers	Right Atrium	heart
42	chr5:58653000-58669400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:58653200-58654600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:58653200-58654800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:58653200-58656000	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr5:58653400-58654400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:58653400-58654400	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr5:58653400-58654600	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr5:58653400-58655600	Weak transcription	Psoas Muscle	Psoas
50	chr5:58653600-58654000	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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