Variant report

Variant	rs1963858
Chromosome Location	chr5:115789599-115789600
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	POLR2A	chr5:115789494-115790558	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF12	chr5:115789492-115791319	SK-N-SH	brain:	n/a	chr5:115791001-115791009 chr5:115790136-115790144 chr5:115790805-115790813
3	GATA3	chr5:115789362-115789806	SH-SY5Y	brain:	n/a	chr5:115789551-115789560 chr5:115789552-115789569
4	TCF12	chr5:115789471-115791405	SK-N-SH	brain:	n/a	chr5:115791001-115791009 chr5:115790136-115790144 chr5:115790805-115790813
5	EP300	chr5:115789546-115791312	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr5:115789449-115791287	SK-N-SH	brain:	n/a	n/a
7	EP300	chr5:115789000-115792048	SK-N-SH	brain:	n/a	n/a
8	TEAD4	chr5:115789508-115791309	SK-N-SH	brain:	n/a	n/a
9	GATA2	chr5:115789331-115789849	SH-SY5Y	brain:	n/a	chr5:115789551-115789560 chr5:115789552-115789569
10	EP300	chr5:115789581-115790008	SK-N-SH_RA	brain:	n/a	n/a
11	GATA3	chr5:115789242-115791260	SK-N-SH	brain:	n/a	chr5:115789551-115789560 chr5:115789552-115789569
12	NFIC	chr5:115789505-115791360	SK-N-SH	brain:	n/a	n/a
13	RXRA	chr5:115789547-115790707	SK-N-SH	brain:	n/a	chr5:115790326-115790335
14	JUND	chr5:115789504-115790673	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr5:115789285-115791494	SK-N-SH	brain:	n/a	chr5:115789551-115789560 chr5:115789552-115789569
16	RAD21	chr5:115789590-115789985	SK-N-SH_RA	brain:	n/a	n/a
17	PBX3	chr5:115789493-115791253	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
SEMA6A	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10058506	0.82[EUR][1000 genomes]
rs171797	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1968362	0.91[ASN][1000 genomes]
rs258017	0.82[EUR][1000 genomes]
rs258018	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs258020	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs26591	0.87[CEU][hapmap]
rs40103	0.88[EUR][1000 genomes]
rs59197344	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7704579	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7728334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

No data

Chromatin state (count:90 , 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	chr5:115781400-115789600	Weak transcription	Primary B cells from cord blood	blood
5	chr5:115782000-115789600	Weak transcription	Fetal Brain Male	brain
6	chr5:115782200-115798200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:115782600-115789800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr5:115783000-115789800	Weak transcription	Fetal Thymus	thymus
9	chr5:115783400-115789800	Weak transcription	Thymus	Thymus
10	chr5:115783400-115790200	Weak transcription	Brain Germinal Matrix	brain
11	chr5:115783400-115790200	Weak transcription	Right Ventricle	heart
12	chr5:115783600-115789600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:115783600-115789600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:115783600-115789800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr5:115783600-115789800	Weak transcription	Fetal Lung	lung
16	chr5:115783600-115790000	Weak transcription	Aorta	Aorta
17	chr5:115783600-115790000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:115783600-115790200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:115783600-115790400	Enhancers	HepG2	liver
20	chr5:115783600-115802200	Weak transcription	Colonic Mucosa	Colon
21	chr5:115783600-115802200	Weak transcription	Pancreas	Pancrea
22	chr5:115783600-115803400	Weak transcription	Esophagus	oesophagus
23	chr5:115783600-115813000	Weak transcription	Spleen	Spleen
24	chr5:115783600-115813200	Weak transcription	Gastric	stomach
25	chr5:115783600-115829600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:115783800-115789600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr5:115783800-115789800	Weak transcription	Adipose Nuclei	Adipose
28	chr5:115783800-115789800	Weak transcription	Ovary	ovary
29	chr5:115783800-115790000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:115783800-115803200	Weak transcription	Liver	Liver
31	chr5:115784000-115791200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:115784200-115796800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:115784200-115800000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:115784400-115791000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
35	chr5:115785000-115790000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr5:115785200-115789800	Weak transcription	Primary T cells from cord blood	blood
37	chr5:115785200-115800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:115785400-115789600	Weak transcription	Left Ventricle	heart
39	chr5:115786400-115789600	Strong transcription	Fetal Muscle Leg	muscle
40	chr5:115787000-115789600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr5:115787000-115789600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:115787200-115789600	Weak transcription	Fetal Intestine Large	intestine
43	chr5:115787600-115791000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr5:115787600-115791000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:115787800-115789600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr5:115787800-115789600	Enhancers	Brain Cingulate Gyrus	brain
47	chr5:115787800-115789600	Enhancers	Brain Hippocampus Middle	brain
48	chr5:115787800-115789600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr5:115787800-115789800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:115787800-115790000	Weak transcription	Fetal Muscle Trunk	muscle

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