Variant report

Variant	rs1947090
Chromosome Location	chr5:58572727-58572728
allele	A/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	EP300	chr5:58572644-58573168	Hela-S3	cervix:	n/a	chr5:58572921-58572931
2	SIN3AK20	chr5:58572690-58573132	PFSK-1	brain:	n/a	n/a
3	STAT3	chr5:58572474-58572872	MCF10A-Er-Src	breast:	n/a	n/a
4	BCL3	chr5:58572632-58573170	A549	lung:	n/a	chr5:58573159-58573168
5	TCF12	chr5:58570995-58573403	A549	lung:	n/a	n/a
6	MAX	chr5:58572592-58573320	A549	lung:	n/a	n/a
7	CEBPB	chr5:58572518-58573209	A549	lung:	n/a	n/a
8	GATA3	chr5:58571048-58573456	A549	lung:	n/a	chr5:58572097-58572107
9	RFX5	chr5:58572708-58573171	Hela-S3	cervix:	n/a	n/a
10	SP1	chr5:58572607-58573274	A549	lung:	n/a	n/a
11	NR3C1	chr5:58572719-58573194	A549	lung:	n/a	n/a
12	BCL3	chr5:58572711-58573276	A549	lung:	n/a	chr5:58573159-58573168
13	NR3C1	chr5:58572724-58573211	A549	lung:	n/a	n/a
14	REST	chr5:58572573-58573108	A549	lung:	n/a	n/a
15	CEBPB	chr5:58572417-58573059	A549	lung:	n/a	chr5:58572502-58572513
16	GATA3	chr5:58572563-58573226	A549	lung:	n/a	n/a
17	JUND	chr5:58572657-58573231	A549	lung:	n/a	chr5:58573165-58573177
18	GATA3	chr5:58572626-58572929	SH-SY5Y	brain:	n/a	n/a
19	CHD2	chr5:58572725-58573114	Hela-S3	cervix:	n/a	n/a
20	FOXA2	chr5:58572618-58573139	A549	lung:	n/a	n/a
21	TAF1	chr5:58572660-58573120	PFSK-1	brain:	n/a	n/a
22	TCF7L2	chr5:58572724-58573164	Hela-S3	cervix:	n/a	n/a
23	GATA3	chr5:58572556-58572995	SK-N-SH	brain:	n/a	n/a
24	CEBPB	chr5:58572626-58573214	Hela-S3	cervix:	n/a	n/a
25	TCF12	chr5:58572622-58573066	A549	lung:	n/a	n/a
26	REST	chr5:58572661-58573044	PFSK-1	brain:	n/a	n/a
27	GTF2F1	chr5:58572683-58573106	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr5:58571211-58573626	Hela-S3	cervix:	n/a	n/a
29	BRCA1	chr5:58572662-58573146	Hela-S3	cervix:	n/a	chr5:58572734-58572741
30	POLR2A	chr5:58572554-58573399	PFSK-1	brain:	n/a	n/a
31	EP300	chr5:58572486-58573452	A549	lung:	n/a	chr5:58572921-58572931
32	TBP	chr5:58571148-58573227	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr5:58572668-58573113	Hela-S3	cervix:	n/a	n/a
34	CEBPB	chr5:58572638-58573120	A549	lung:	n/a	n/a
35	POLR2A	chr5:58572554-58573206	PFSK-1	brain:	n/a	n/a
36	RAD21	chr5:58572707-58573242	Hela-S3	cervix:	n/a	n/a
37	GATA3	chr5:58572544-58573096	SK-N-SH	brain:	n/a	n/a
38	EP300	chr5:58572467-58573395	A549	lung:	n/a	chr5:58572921-58572931
39	MAX	chr5:58572686-58573224	A549	lung:	n/a	n/a
40	POLR2A	chr5:58570997-58573240	Hela-S3	cervix:	n/a	n/a
41	RCOR1	chr5:58572685-58573033	Hela-S3	cervix:	n/a	n/a
42	SP1	chr5:58572486-58573373	A549	lung:	n/a	n/a
43	GATA2	chr5:58572603-58572943	SH-SY5Y	brain:	n/a	n/a
44	ETS1	chr5:58572590-58573099	A549	lung:	n/a	n/a
45	FOXA2	chr5:58572608-58573263	A549	lung:	n/a	n/a
46	NR3C1	chr5:58572714-58573236	A549	lung:	n/a	n/a
47	FOSL2	chr5:58572592-58573189	A549	lung:	n/a	chr5:58573165-58573177
48	NR3C1	chr5:58572702-58573207	A549	lung:	n/a	n/a
49	NR3C1	chr5:58572642-58573187	A549	lung:	n/a	n/a
50	POLR2A	chr5:58572607-58573170	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:59327949..59328466-chr5:58571972..58572886,2	Hela-S3	cervix:

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1031197	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10491352	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10940644	0.80[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11954668	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11959132	0.80[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11959567	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12189022	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12518773	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12519611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12521263	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12522944	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1445948	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1445952	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1445954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1579848	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1579849	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16889479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16889499	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16889518	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444185	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17528522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17528578	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17780175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1823070	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1838733	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1840846	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867711	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1867712	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1947095	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2021775	1.00[JPT][hapmap]
rs2028836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2081106	1.00[JPT][hapmap]
rs2409631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4700325	1.00[JPT][hapmap]
rs4700328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858946	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6877508	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888028	0.81[ASN][1000 genomes]
rs6891161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7703022	1.00[CHB][hapmap]
rs7717303	0.81[ASN][1000 genomes]
rs7719441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58568200-58572800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr5:58568200-58572800	Active TSS	Stomach Smooth Muscle	stomach
3	chr5:58571000-58573800	Enhancers	Fetal Heart	heart
4	chr5:58571800-58579400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:58572000-58572800	Weak transcription	Colonic Mucosa	Colon
6	chr5:58572000-58572800	Flanking Active TSS	Fetal Kidney	kidney
7	chr5:58572000-58572800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:58572000-58572800	Weak transcription	Right Ventricle	heart
9	chr5:58572000-58572800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:58572000-58573000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr5:58572000-58573000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:58572000-58573200	Enhancers	Brain Germinal Matrix	brain
13	chr5:58572000-58573400	Enhancers	Colon Smooth Muscle	Colon
14	chr5:58572000-58573600	Enhancers	Fetal Brain Male	brain
15	chr5:58572000-58573800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr5:58572000-58582800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:58572200-58572800	Weak transcription	Brain Anterior Caudate	brain
18	chr5:58572200-58572800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:58572200-58572800	Enhancers	Fetal Intestine Large	intestine
20	chr5:58572200-58572800	Weak transcription	Fetal Stomach	stomach
21	chr5:58572200-58572800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr5:58572200-58573000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr5:58572200-58573000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:58572200-58573000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr5:58572200-58573000	Weak transcription	Adipose Nuclei	Adipose
26	chr5:58572200-58573200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:58572200-58573200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr5:58572200-58573200	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr5:58572200-58573200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:58572200-58573200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr5:58572200-58573200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:58572200-58573600	Enhancers	Fetal Lung	lung
33	chr5:58572200-58573800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:58572200-58573800	Enhancers	Brain Hippocampus Middle	brain
35	chr5:58572200-58573800	Enhancers	Brain Substantia Nigra	brain
36	chr5:58572200-58574400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:58572200-58583000	Weak transcription	Left Ventricle	heart
38	chr5:58572400-58572800	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr5:58572400-58572800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr5:58572400-58572800	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr5:58572400-58572800	Enhancers	HUVEC	blood vessel
42	chr5:58572400-58573000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr5:58572400-58573000	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr5:58572400-58573000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr5:58572400-58573000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:58572400-58573200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr5:58572400-58573200	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr5:58572400-58573200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:58572400-58573200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr5:58572400-58573200	Enhancers	Stomach Mucosa	stomach

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