Variant report

Variant	rs12740779
Chromosome Location	chr1:94053973-94053974
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	NR3C1	chr1:94053775-94054138	A549	lung:	n/a	chr1:94054005-94054021 chr1:94054005-94054021
2	MYC	chr1:94053664-94054129	NB4	blood:	n/a	chr1:94053847-94053856
3	GABPA	chr1:94053804-94054107	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:94053852-94053982	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:94052809-94055652	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:94053363-94054402	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:94053903-94054107	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:94053626-94054458	Hela-S3	cervix:	n/a	n/a
9	FOS	chr1:94053745-94054132	HUVEC	blood vessel:	n/a	chr1:94053932-94053941 chr1:94053931-94053941 chr1:94053930-94053941 chr1:94053932-94053939
10	JUND	chr1:94053807-94054074	K562	blood:	n/a	chr1:94053932-94053941 chr1:94053931-94053941 chr1:94053932-94053939
11	USF2	chr1:94053784-94054431	Hela-S3	cervix:	n/a	n/a
12	MYC	chr1:94053941-94053989	HUVEC	blood vessel:	n/a	n/a
13	FOS	chr1:94053878-94053995	MCF10A-Er-Src	breast:	n/a	chr1:94053932-94053941 chr1:94053931-94053941 chr1:94053930-94053941 chr1:94053932-94053939
14	MAX	chr1:94053572-94054230	NB4	blood:	n/a	chr1:94053847-94053856
15	POLR2A	chr1:94053770-94054074	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94053174..94055459-chr1:94085233..94086891,2	MCF-7	breast:
2	chr1:94031866..94034808-chr1:94053760..94055663,2	K562	blood:

Variant related genes	Relation type
ENSG00000224093	TF binding region
BCAR3	TF binding region
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11576435	1.00[ASN][1000 genomes]
rs11577352	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579004	1.00[ASN][1000 genomes]
rs11579685	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580965	1.00[ASN][1000 genomes]
rs11588860	1.00[ASN][1000 genomes]
rs12066343	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073093	1.00[ASN][1000 genomes]
rs12090736	1.00[ASN][1000 genomes]
rs12732557	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739747	1.00[ASN][1000 genomes]
rs12744941	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757325	1.00[ASN][1000 genomes]
rs12760092	1.00[ASN][1000 genomes]
rs17110063	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110101	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110111	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110225	1.00[ASN][1000 genomes]
rs17110370	1.00[ASN][1000 genomes]
rs1877603	1.00[ASN][1000 genomes]
rs1877604	1.00[ASN][1000 genomes]
rs1891138	1.00[ASN][1000 genomes]
rs2818163	1.00[ASN][1000 genomes]
rs34183660	1.00[ASN][1000 genomes]
rs34423897	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34663884	1.00[ASN][1000 genomes]
rs34666525	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34726063	1.00[ASN][1000 genomes]
rs35126293	1.00[ASN][1000 genomes]
rs35691338	1.00[ASN][1000 genomes]
rs35896714	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35972761	1.00[ASN][1000 genomes]
rs36115605	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3950119	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59996315	1.00[ASN][1000 genomes]
rs61780979	1.00[ASN][1000 genomes]
rs61780999	1.00[ASN][1000 genomes]
rs6660968	1.00[ASN][1000 genomes]
rs6666778	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677770	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679609	1.00[ASN][1000 genomes]
rs6683296	1.00[ASN][1000 genomes]
rs66966060	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67043929	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67300695	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67354439	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67511232	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71652539	1.00[ASN][1000 genomes]
rs72721041	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511890	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525880	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531106	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543098	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543734	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7543763	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553185	1.00[ASN][1000 genomes]
rs7555302	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761802	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[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	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94025600-94073800	Weak transcription	Fetal Brain Female	brain
2	chr1:94038400-94054000	Weak transcription	Brain Substantia Nigra	brain
3	chr1:94038400-94054800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:94038600-94054200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:94040000-94055000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:94041800-94059400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:94042000-94054800	Weak transcription	Primary B cells from cord blood	blood
8	chr1:94042200-94063200	Weak transcription	Brain Germinal Matrix	brain
9	chr1:94043000-94058400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:94046600-94058200	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:94048200-94054600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:94048200-94059200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:94048200-94059400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:94048400-94059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:94048600-94064200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:94049600-94059400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:94050000-94054800	Weak transcription	GM12878-XiMat	blood
18	chr1:94050000-94056200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:94050000-94059400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:94050600-94055600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:94050800-94054600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:94050800-94057800	Weak transcription	Small Intestine	intestine
23	chr1:94050800-94059200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:94051000-94054200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:94051000-94056800	Weak transcription	Fetal Thymus	thymus
26	chr1:94051200-94057200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:94051200-94057200	Weak transcription	Fetal Kidney	kidney
28	chr1:94051400-94054400	Weak transcription	Brain Anterior Caudate	brain
29	chr1:94051400-94057600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:94051600-94055400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:94051600-94055800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:94051800-94054000	Strong transcription	Lung	lung
33	chr1:94051800-94054400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:94051800-94055000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr1:94051800-94055400	Weak transcription	Stomach Mucosa	stomach
36	chr1:94051800-94055800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:94051800-94056400	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr1:94052000-94055200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:94052000-94055800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:94052000-94055800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:94052000-94056000	Strong transcription	Fetal Lung	lung
42	chr1:94052000-94056400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:94052000-94056800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:94052000-94057400	Weak transcription	Colonic Mucosa	Colon
45	chr1:94052200-94056000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:94052400-94054000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:94052400-94054800	Genic enhancers	Left Ventricle	heart
48	chr1:94052400-94055000	Strong transcription	Liver	Liver
49	chr1:94052400-94055800	Strong transcription	A549	lung
50	chr1:94052400-94057600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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