Variant report

Variant	rs66961454
Chromosome Location	chr1:94790635-94790636
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	FOXM1	chr1:94790538-94792201	ECC-1	luminal epithelium:	n/a	n/a
2	SP1	chr1:94790546-94792480	HCT-116	colon:	n/a	chr1:94791610-94791624 chr1:94791610-94791620 chr1:94791611-94791620
3	TCF12	chr1:94790611-94792143	A549	lung:	n/a	chr1:94791961-94791970
4	POLR2A	chr1:94788372-94793300	HUVEC	blood vessel:	n/a	n/a
5	NFIC	chr1:94790613-94792283	ECC-1	luminal epithelium:	n/a	chr1:94791323-94791351
6	NFIC	chr1:94790496-94792356	ECC-1	luminal epithelium:	n/a	chr1:94791323-94791351
7	POLR2A	chr1:94790307-94792256	HUVEC	blood vessel:	n/a	n/a
8	FOSL1	chr1:94790405-94791925	HCT-116	colon:	n/a	chr1:94791573-94791580
9	TCF12	chr1:94790580-94792430	SK-N-SH	brain:	n/a	chr1:94792263-94792271 chr1:94791961-94791970
10	EP300	chr1:94790516-94792184	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr1:94790597-94792356	SK-N-SH	brain:	n/a	chr1:94791323-94791351
12	FOXM1	chr1:94790572-94791926	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr1:94790599-94792286	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr1:94790583-94792432	SK-N-SH	brain:	n/a	chr1:94792041-94792048 chr1:94792034-94792055 chr1:94792041-94792048 chr1:94792036-94792052 chr1:94792041-94792048

Variant related genes	Relation type
ENSG00000236098	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1054626	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11165103	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165114	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12022859	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12024941	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12027548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031606	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12036085	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038745	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12039546	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12042509	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046536	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12093742	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12562103	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12563826	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360365	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1576592	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1611832	0.94[EUR][1000 genomes]
rs1622451	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1623248	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1623314	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1629275	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1687947	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1687950	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16928	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17111408	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17111426	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111436	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1765636	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1765640	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1929131	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1999270	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1999271	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2130899	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391472	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35275815	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3789690	0.83[EUR][1000 genomes]
rs4543802	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4847201	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4847296	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55961421	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56037795	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57666908	0.83[EUR][1000 genomes]
rs6541343	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6541345	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6662877	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6673491	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6675959	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6681827	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66918029	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67180557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67554381	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67612304	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67681803	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67807923	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68193246	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7413345	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7415246	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7515965	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7520754	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7525320	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7533977	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7554714	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428510	chr1:94709575-94866655	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr1:94783200-94792800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:94784400-94791000	Weak transcription	Gastric	stomach
3	chr1:94784800-94791400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:94785400-94792000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:94785600-94792200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:94785800-94790800	Weak transcription	Fetal Heart	heart
7	chr1:94785800-94790800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:94785800-94791200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:94785800-94791600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:94785800-94791800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:94787000-94790800	Enhancers	HSMMtube	muscle
12	chr1:94787200-94790800	Enhancers	Hela-S3	cervix
13	chr1:94787200-94791400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:94787200-94791400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:94787200-94795200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:94787800-94790800	Enhancers	Osteobl	bone
17	chr1:94787800-94793400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr1:94788400-94790800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:94788400-94791000	Weak transcription	Adipose Nuclei	Adipose
20	chr1:94788400-94791400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr1:94788400-94792000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:94788400-94792600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:94788400-94794000	Enhancers	NHLF	lung
24	chr1:94788600-94790800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:94788600-94790800	Weak transcription	Stomach Mucosa	stomach
26	chr1:94788600-94792000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:94788600-94792000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:94788600-94792000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:94788600-94792000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:94788600-94800800	Weak transcription	Pancreas	Pancrea
31	chr1:94788800-94791000	Weak transcription	HepG2	liver
32	chr1:94788800-94792000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:94789000-94792800	Enhancers	Fetal Kidney	kidney
34	chr1:94789400-94790800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:94789400-94790800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:94789400-94790800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:94789400-94791200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:94789400-94792000	Enhancers	HSMM	muscle
39	chr1:94789600-94790800	Weak transcription	Aorta	Aorta
40	chr1:94789600-94790800	Weak transcription	Right Atrium	heart
41	chr1:94789800-94791200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr1:94789800-94793000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:94790000-94791000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:94790200-94790800	Enhancers	A549	lung
45	chr1:94790200-94790800	Enhancers	NHEK	skin
46	chr1:94790200-94791000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:94790200-94792400	Enhancers	NHDF-Ad	bronchial
48	chr1:94790200-94796000	Enhancers	HMEC	breast
49	chr1:94790400-94790800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:94790400-94790800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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