Variant report

Variant	rs7728334
Chromosome Location	chr5:115790315-115790316
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	GATA2	chr5:115790180-115790546	SH-SY5Y	brain:	n/a	n/a
2	WRNIP1	chr5:115790049-115790541	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:115790126-115790710	HL-60	blood:	n/a	n/a
4	EP300	chr5:115790069-115790645	SK-N-SH_RA	brain:	n/a	n/a
5	GATA3	chr5:115790293-115790501	SH-SY5Y	brain:	n/a	n/a
6	FOXP2	chr5:115790143-115790579	SK-N-MC	brain:	n/a	n/a
7	RUNX3	chr5:115789985-115790615	GM12878	blood:	n/a	n/a
8	SPI1	chr5:115790118-115790477	GM12891	blood:	n/a	n/a
9	IRF4	chr5:115790089-115790562	GM12878	blood:	n/a	n/a
10	YY1	chr5:115790121-115790610	SK-N-SH_RA	brain:	n/a	n/a
11	POLR2A	chr5:115789494-115790558	H1-hESC	embryonic stem cell:	n/a	n/a
12	MYC	chr5:115790187-115790560	NB4	blood:	n/a	n/a
13	BCL3	chr5:115790040-115790474	GM12878	blood:	n/a	chr5:115790326-115790335
14	REST	chr5:115790132-115790599	PFSK-1	brain:	n/a	n/a
15	RAD21	chr5:115790085-115790574	SK-N-SH_RA	brain:	n/a	n/a
16	TCF12	chr5:115789492-115791319	SK-N-SH	brain:	n/a	chr5:115791001-115791009 chr5:115790136-115790144 chr5:115790805-115790813
17	TCF12	chr5:115789471-115791405	SK-N-SH	brain:	n/a	chr5:115791001-115791009 chr5:115790136-115790144 chr5:115790805-115790813
18	BCL11A	chr5:115790094-115790564	GM12878	blood:	n/a	chr5:115790326-115790335
19	SIN3AK20	chr5:115790259-115790533	PFSK-1	brain:	n/a	n/a
20	MEF2A	chr5:115790103-115790510	GM12878	blood:	n/a	n/a
21	MAX	chr5:115790088-115790633	SK-N-SH	brain:	n/a	n/a
22	MXI1	chr5:115790050-115790507	GM12878	blood:	n/a	n/a
23	CEBPB	chr5:115790092-115790669	GM12878	blood:	n/a	n/a
24	BATF	chr5:115790156-115790464	GM12878	blood:	n/a	n/a
25	SPI1	chr5:115790256-115790413	GM12878	blood:	n/a	n/a
26	EP300	chr5:115789546-115791312	SK-N-SH	brain:	n/a	n/a
27	POU2F2	chr5:115790054-115790524	GM12891	blood:	n/a	n/a
28	TAF1	chr5:115790212-115790471	SK-N-SH	brain:	n/a	n/a
29	FOXM1	chr5:115790136-115790559	GM12878	blood:	n/a	n/a
30	PBX3	chr5:115789449-115791287	SK-N-SH	brain:	n/a	n/a
31	REST	chr5:115790100-115790578	PFSK-1	brain:	n/a	n/a
32	POU2F2	chr5:115790125-115790447	GM12891	blood:	n/a	n/a
33	ATF1	chr5:115790232-115790432	K562	blood:	n/a	n/a
34	SPI1	chr5:115790246-115790552	HL-60	blood:	n/a	n/a
35	ZNF143	chr5:115790064-115790448	GM12878	blood:	n/a	n/a
36	POLR2A	chr5:115790115-115790611	SK-N-MC	brain:	n/a	n/a
37	RELA	chr5:115790101-115790541	GM19099	blood:	n/a	n/a
38	EP300	chr5:115789000-115792048	SK-N-SH	brain:	n/a	n/a
39	YY1	chr5:115790129-115790572	SK-N-SH_RA	brain:	n/a	n/a
40	POLR2A	chr5:115790271-115790650	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr5:115790227-115790559	HL-60	blood:	n/a	n/a
42	YY1	chr5:115790216-115790516	GM12878	blood:	n/a	n/a
43	ATF2	chr5:115790075-115790574	GM12878	blood:	n/a	n/a
44	TEAD4	chr5:115789508-115791309	SK-N-SH	brain:	n/a	n/a
45	MAX	chr5:115790143-115790581	NB4	blood:	n/a	n/a
46	POLR2A	chr5:115790099-115790604	PFSK-1	brain:	n/a	n/a
47	IKZF1	chr5:115790026-115790630	GM12878	blood:	n/a	n/a
48	ELF1	chr5:115790079-115790526	GM12878	blood:	n/a	n/a
49	NFIC	chr5:115789982-115790551	GM12878	blood:	n/a	n/a
50	GATA3	chr5:115789242-115791260	SK-N-SH	brain:	n/a	chr5:115789551-115789560 chr5:115789552-115789569

Variant related genes	Relation type
SEMA6A	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10058506	0.82[EUR][1000 genomes]
rs171797	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1963858	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1968362	0.92[ASN][1000 genomes]
rs258017	0.82[EUR][1000 genomes]
rs258018	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs258020	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs40103	0.88[EUR][1000 genomes]
rs59197344	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7704579	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115774600-115811000	Weak transcription	Small Intestine	intestine
2	chr5:115782200-115798200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:115783600-115790400	Enhancers	HepG2	liver
4	chr5:115783600-115802200	Weak transcription	Colonic Mucosa	Colon
5	chr5:115783600-115802200	Weak transcription	Pancreas	Pancrea
6	chr5:115783600-115803400	Weak transcription	Esophagus	oesophagus
7	chr5:115783600-115813000	Weak transcription	Spleen	Spleen
8	chr5:115783600-115813200	Weak transcription	Gastric	stomach
9	chr5:115783600-115829600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:115783800-115803200	Weak transcription	Liver	Liver
11	chr5:115784000-115791200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:115784200-115796800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:115784200-115800000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:115784400-115791000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
15	chr5:115785200-115800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:115787600-115791000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:115787600-115791000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:115787800-115791600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:115788000-115813200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:115788400-115791800	Enhancers	Fetal Stomach	stomach
21	chr5:115788400-115792000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
22	chr5:115788600-115790800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:115788600-115791000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:115788600-115791400	Enhancers	HSMM	muscle
25	chr5:115788600-115793800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:115788800-115791400	Enhancers	HSMMtube	muscle
27	chr5:115789000-115791000	Enhancers	Fetal Brain Female	brain
28	chr5:115789000-115791200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr5:115789000-115791600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:115789000-115793800	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr5:115789000-115795600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:115789000-115797400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr5:115789000-115800200	Weak transcription	Psoas Muscle	Psoas
34	chr5:115789200-115790800	Enhancers	Primary B cells from peripheral blood	blood
35	chr5:115789200-115791800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
36	chr5:115789200-115796000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:115789400-115795200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:115789600-115790400	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr5:115789600-115790600	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr5:115789600-115790600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr5:115789600-115791000	Enhancers	Primary B cells from cord blood	blood
42	chr5:115789600-115791000	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr5:115789600-115791000	Enhancers	Fetal Brain Male	brain
44	chr5:115789600-115791000	Genic enhancers	Fetal Muscle Leg	muscle
45	chr5:115789600-115791000	Enhancers	Left Ventricle	heart
46	chr5:115789600-115791400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr5:115789600-115792000	Enhancers	Primary hematopoietic stem cells	blood
48	chr5:115789600-115792400	Enhancers	Rectal Smooth Muscle	rectum
49	chr5:115789600-115795400	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr5:115789600-115812600	Strong transcription	Fetal Intestine Large	intestine

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