Variant report

Variant	rs1963859
Chromosome Location	chr5:115789729-115789730
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	POLR2A	chr5:115789606-115790023	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr5:115789494-115790558	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:115789634-115789853	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr5:115789492-115791319	SK-N-SH	brain:	n/a	chr5:115791001-115791009 chr5:115790136-115790144 chr5:115790805-115790813
5	GATA3	chr5:115789362-115789806	SH-SY5Y	brain:	n/a	chr5:115789551-115789560 chr5:115789552-115789569
6	TCF12	chr5:115789471-115791405	SK-N-SH	brain:	n/a	chr5:115791001-115791009 chr5:115790136-115790144 chr5:115790805-115790813
7	EP300	chr5:115789546-115791312	SK-N-SH	brain:	n/a	n/a
8	PBX3	chr5:115789449-115791287	SK-N-SH	brain:	n/a	n/a
9	EP300	chr5:115789609-115789971	SK-N-SH_RA	brain:	n/a	n/a
10	EP300	chr5:115789000-115792048	SK-N-SH	brain:	n/a	n/a
11	TEAD4	chr5:115789508-115791309	SK-N-SH	brain:	n/a	n/a
12	YY1	chr5:115789696-115790030	SK-N-SH_RA	brain:	n/a	chr5:115789964-115789972
13	USF1	chr5:115789706-115789963	SK-N-SH_RA	brain:	n/a	n/a
14	FOXA1	chr5:115789643-115789957	HepG2	liver:	n/a	n/a
15	GATA2	chr5:115789331-115789849	SH-SY5Y	brain:	n/a	chr5:115789551-115789560 chr5:115789552-115789569
16	EP300	chr5:115789581-115790008	SK-N-SH_RA	brain:	n/a	n/a
17	GATA3	chr5:115789242-115791260	SK-N-SH	brain:	n/a	chr5:115789551-115789560 chr5:115789552-115789569
18	ARID3A	chr5:115789701-115789914	HepG2	liver:	n/a	n/a
19	PBX3	chr5:115789683-115789873	GM12878	blood:	n/a	n/a
20	FOXP2	chr5:115789676-115789959	PFSK-1	brain:	n/a	n/a
21	NFIC	chr5:115789505-115791360	SK-N-SH	brain:	n/a	n/a
22	RXRA	chr5:115789547-115790707	SK-N-SH	brain:	n/a	chr5:115790326-115790335
23	RUNX3	chr5:115789601-115790654	GM12878	blood:	n/a	chr5:115789842-115789859
24	JUND	chr5:115789504-115790673	SK-N-SH	brain:	n/a	n/a
25	GATA3	chr5:115789285-115791494	SK-N-SH	brain:	n/a	chr5:115789551-115789560 chr5:115789552-115789569
26	RAD21	chr5:115789590-115789985	SK-N-SH_RA	brain:	n/a	n/a
27	PBX3	chr5:115789493-115791253	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
SEMA6A	TF binding region

rs_ID	r²[population]
rs13360956	1.00[EUR][1000 genomes]
rs17139822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1863988	1.00[EUR][1000 genomes]
rs57331771	1.00[EUR][1000 genomes]
rs58112531	1.00[EUR][1000 genomes]
rs59453842	1.00[EUR][1000 genomes]
rs59710297	1.00[EUR][1000 genomes]
rs59909017	1.00[EUR][1000 genomes]
rs60032314	1.00[EUR][1000 genomes]
rs60372854	1.00[EUR][1000 genomes]
rs60456887	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73263025	1.00[EUR][1000 genomes]
rs73263035	1.00[EUR][1000 genomes]
rs73263038	1.00[EUR][1000 genomes]
rs73263042	1.00[EUR][1000 genomes]
rs73263052	1.00[EUR][1000 genomes]
rs73263062	1.00[EUR][1000 genomes]
rs73263071	1.00[EUR][1000 genomes]
rs73263076	1.00[EUR][1000 genomes]
rs73264977	1.00[EUR][1000 genomes]
rs73264993	1.00[EUR][1000 genomes]
rs73266806	1.00[EUR][1000 genomes]
rs73266807	1.00[EUR][1000 genomes]
rs73266818	1.00[EUR][1000 genomes]
rs73266825	1.00[EUR][1000 genomes]
rs73266826	1.00[EUR][1000 genomes]
rs73266833	1.00[EUR][1000 genomes]
rs73266838	1.00[EUR][1000 genomes]
rs73266848	1.00[EUR][1000 genomes]
rs73268917	1.00[EUR][1000 genomes]
rs73268920	1.00[EUR][1000 genomes]
rs73268927	1.00[EUR][1000 genomes]
rs73268929	1.00[EUR][1000 genomes]
rs73268944	1.00[EUR][1000 genomes]
rs73268948	1.00[EUR][1000 genomes]
rs73268952	1.00[EUR][1000 genomes]
rs73268959	1.00[EUR][1000 genomes]
rs73268964	1.00[EUR][1000 genomes]
rs73268967	1.00[EUR][1000 genomes]
rs73268975	1.00[EUR][1000 genomes]
rs73268979	1.00[EUR][1000 genomes]
rs73268984	1.00[EUR][1000 genomes]
rs73268993	1.00[EUR][1000 genomes]
rs73270707	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73270746	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115774600-115811000	Weak transcription	Small Intestine	intestine
2	chr5:115778000-115790000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr5:115779000-115789800	Strong transcription	Placenta	Placenta
4	chr5:115782200-115798200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:115782600-115789800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr5:115783000-115789800	Weak transcription	Fetal Thymus	thymus
7	chr5:115783400-115789800	Weak transcription	Thymus	Thymus
8	chr5:115783400-115790200	Weak transcription	Brain Germinal Matrix	brain
9	chr5:115783400-115790200	Weak transcription	Right Ventricle	heart
10	chr5:115783600-115789800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:115783600-115789800	Weak transcription	Fetal Lung	lung
12	chr5:115783600-115790000	Weak transcription	Aorta	Aorta
13	chr5:115783600-115790000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:115783600-115790200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:115783600-115790400	Enhancers	HepG2	liver
16	chr5:115783600-115802200	Weak transcription	Colonic Mucosa	Colon
17	chr5:115783600-115802200	Weak transcription	Pancreas	Pancrea
18	chr5:115783600-115803400	Weak transcription	Esophagus	oesophagus
19	chr5:115783600-115813000	Weak transcription	Spleen	Spleen
20	chr5:115783600-115813200	Weak transcription	Gastric	stomach
21	chr5:115783600-115829600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr5:115783800-115789800	Weak transcription	Adipose Nuclei	Adipose
23	chr5:115783800-115789800	Weak transcription	Ovary	ovary
24	chr5:115783800-115790000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr5:115783800-115803200	Weak transcription	Liver	Liver
26	chr5:115784000-115791200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:115784200-115796800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:115784200-115800000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:115784400-115791000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
30	chr5:115785000-115790000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr5:115785200-115789800	Weak transcription	Primary T cells from cord blood	blood
32	chr5:115785200-115800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:115787600-115791000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr5:115787600-115791000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:115787800-115789800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:115787800-115790000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr5:115787800-115791600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:115788000-115813200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:115788400-115791800	Enhancers	Fetal Stomach	stomach
40	chr5:115788400-115792000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
41	chr5:115788600-115789800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr5:115788600-115789800	Enhancers	Brain Substantia Nigra	brain
43	chr5:115788600-115790000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:115788600-115790000	Enhancers	Fetal Heart	heart
45	chr5:115788600-115790200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr5:115788600-115790200	Enhancers	Fetal Kidney	kidney
47	chr5:115788600-115790800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:115788600-115791000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:115788600-115791400	Enhancers	HSMM	muscle
50	chr5:115788600-115793800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell

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