Variant report

Variant	rs11161583
Chromosome Location	chr1:85742861-85742862
allele	A/C
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	SRF	chr1:85741461-85743025	HCT-116	colon:	n/a	n/a
2	CREB1	chr1:85741866-85742881	ECC-1	luminal epithelium:	n/a	n/a
3	GABPA	chr1:85741658-85742949	SK-N-SH	brain:	n/a	chr1:85741945-85741954 chr1:85741911-85741918
4	POLR2A	chr1:85740468-85743570	PANC-1	pancreas:	n/a	n/a
5	EBF1	chr1:85742052-85742879	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:85740591-85742964	GM12891	blood:	n/a	n/a
7	SRF	chr1:85741870-85742978	MCF-7	breast:	n/a	n/a
8	ELF1	chr1:85741515-85742975	HCT-116	colon:	n/a	chr1:85742651-85742662 chr1:85742210-85742219 chr1:85742209-85742222 chr1:85742343-85742355
9	STAT3	chr1:85742555-85742909	GM12878	blood:	n/a	chr1:85742770-85742781
10	KAP1	chr1:85740518-85742974	HEK293	kidney:	n/a	chr1:85741050-85741059
11	RELA	chr1:85740582-85742917	GM12878	blood:	n/a	chr1:85741485-85741494 chr1:85741485-85741494
12	POLR2A	chr1:85741369-85742939	Raji	blood:	n/a	n/a
13	MTA3	chr1:85741236-85742914	GM12878	blood:	n/a	n/a
14	HEY1	chr1:85741619-85742871	HepG2	liver:	n/a	chr1:85741928-85741943 chr1:85742088-85742103 chr1:85742080-85742095
15	MYC	chr1:85741486-85742880	NB4	blood:	n/a	chr1:85741944-85741954
16	POLR2A	chr1:85740603-85742874	K562	blood:	n/a	n/a
17	HCFC1	chr1:85740700-85743065	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:85741682-85742910	U87	brain:	n/a	n/a
19	POLR2A	chr1:85740638-85742911	GM12878	blood:	n/a	n/a
20	TBP	chr1:85742053-85742898	GM12878	blood:	n/a	n/a
21	KAP1	chr1:85742084-85742961	U2OS	brain:	n/a	n/a
22	CREB1	chr1:85741729-85742871	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:85741248-85742904	GM18505	blood:	n/a	n/a
24	POLR2A	chr1:85740399-85742970	HUVEC	blood vessel:	n/a	n/a
25	FOSL2	chr1:85742467-85742926	A549	lung:	n/a	n/a
26	POLR2A	chr1:85741380-85742868	GM19193	blood:	n/a	n/a
27	NRF1	chr1:85741319-85743124	SK-N-SH	brain:	n/a	chr1:85741945-85741954 chr1:85742461-85742472 chr1:85741911-85741918
28	POLR2A	chr1:85741471-85742957	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:85741239-85742952	PBDE	blood:	n/a	n/a
30	SIN3AK20	chr1:85742359-85743070	PANC-1	pancreas:	n/a	n/a
31	SRF	chr1:85741576-85743216	HCT-116	colon:	n/a	n/a
32	MAX	chr1:85741848-85742906	A549	lung:	n/a	chr1:85741944-85741954
33	TCF12	chr1:85741745-85742883	ECC-1	luminal epithelium:	n/a	chr1:85742548-85742555
34	MBD4	chr1:85742397-85742934	HepG2	liver:	n/a	n/a
35	PML	chr1:85741239-85742947	GM12878	blood:	n/a	n/a
36	MXI1	chr1:85741193-85742945	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:85741489-85742862	K562	blood:	n/a	n/a
38	SRF	chr1:85741863-85742972	MCF-7	breast:	n/a	n/a
39	STAT3	chr1:85742503-85742863	MCF10A-Er-Src	breast:	n/a	chr1:85742770-85742781
40	POLR2A	chr1:85741243-85742877	GM19099	blood:	n/a	n/a
41	MXI1	chr1:85741379-85742886	HepG2	liver:	n/a	n/a
42	FOS	chr1:85741620-85742891	HUVEC	blood vessel:	n/a	chr1:85742085-85742094 chr1:85741946-85741955
43	POLR2A	chr1:85740800-85743131	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr1:85741255-85742865	GM18951	blood:	n/a	n/a
45	POLR2A	chr1:85741274-85743242	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr1:85741994-85742879	SK-N-MC	brain:	n/a	n/a
47	BRCA1	chr1:85742012-85742898	Hela-S3	cervix:	n/a	n/a
48	BHLHE40	chr1:85742073-85742891	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:85741164-85742956	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAZ	chr1:85740442-85742959	IMR90	lung:	n/a	chr1:85741944-85741954

No.	Distal block	Cell Line	Cell type
1	chr1:85739753..85743262-chr1:86045535..86049012,3	K562	blood:
2	chr1:85742187..85745018-chr1:85749555..85753087,3	K562	blood:
3	chr1:85742188..85743029-chr1:149223809..149224656,2	Hela-S3	cervix:
4	chr1:85665913..85668656-chr1:85741362..85743092,3	MCF-7	breast:
5	chr1:85665631..85669772-chr1:85739485..85744059,5	K562	blood:
6	chr1:85722628..85726570-chr1:85740869..85744448,4	MCF-7	breast:
7	chr1:85723214..85729954-chr1:85738689..85743771,11	K562	blood:
8	chr1:85665227..85667257-chr1:85740935..85743875,2	K562	blood:
9	chr1:85741905..85744580-chr1:85747619..85751624,6	K562	blood:
10	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:

Variant related genes	Relation type
BCL10	TF binding region
ENSG00000223653	TF binding region
ENSG00000206737	Chromatin interaction
ENSG00000264380	Chromatin interaction
ENSG00000097096	Chromatin interaction
ENSG00000153904	Chromatin interaction
ENSG00000272691	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000162642	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1060843	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161564	0.92[ASN][1000 genomes]
rs11161581	0.96[ASN][1000 genomes]
rs12065528	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12066982	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12068389	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12068788	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12084232	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12086970	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12087340	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12562182	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12563515	0.96[ASN][1000 genomes]
rs12726649	0.96[ASN][1000 genomes]
rs12743302	0.92[ASN][1000 genomes]
rs12744565	0.96[ASN][1000 genomes]
rs12746169	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17124345	0.92[ASN][1000 genomes]
rs35486093	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35783363	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35798604	0.92[ASN][1000 genomes]
rs36116171	0.96[ASN][1000 genomes]
rs4074156	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4258258	0.92[ASN][1000 genomes]
rs6693229	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9887811	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9887812	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9887879	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85739200-85743000	Active TSS	Psoas Muscle	Psoas
2	chr1:85740200-85743200	Active TSS	Colonic Mucosa	Colon
3	chr1:85740600-85743000	Active TSS	Right Atrium	heart
4	chr1:85740600-85743000	Active TSS	Right Ventricle	heart
5	chr1:85740600-85743200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:85740600-85743200	Active TSS	Esophagus	oesophagus
7	chr1:85740800-85743000	Active TSS	Aorta	Aorta
8	chr1:85740800-85743400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr1:85741000-85743000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:85741000-85743000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:85741000-85743000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:85741000-85743000	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr1:85741000-85743000	Active TSS	Fetal Muscle Leg	muscle
14	chr1:85741000-85743200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr1:85741000-85743200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:85741000-85743200	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr1:85741200-85743000	Active TSS	H1 Cell Line	embryonic stem cell
18	chr1:85741200-85743000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:85741200-85743000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:85741200-85743000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:85741200-85743000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:85741200-85743000	Active TSS	Colon Smooth Muscle	Colon
23	chr1:85741200-85743000	Active TSS	Fetal Muscle Trunk	muscle
24	chr1:85741200-85743200	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr1:85741200-85743200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:85741200-85743400	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:85741400-85743000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:85741400-85743000	Active TSS	Fetal Brain Female	brain
29	chr1:85741400-85743200	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr1:85741400-85743200	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr1:85741400-85743200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:85741400-85743200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:85741400-85743200	Active TSS	Duodenum Mucosa	Duodenum
34	chr1:85741400-85743200	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr1:85741600-85743000	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr1:85741600-85743000	Active TSS	Fetal Stomach	stomach
37	chr1:85741600-85743200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:85741600-85743200	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr1:85741600-85743200	Active TSS	Brain Anterior Caudate	brain
40	chr1:85741600-85743200	Active TSS	Rectal Smooth Muscle	rectum
41	chr1:85741600-85743200	Active TSS	Thymus	Thymus
42	chr1:85741800-85743000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:85741800-85743000	Active TSS	Brain Angular Gyrus	brain
44	chr1:85741800-85743000	Active TSS	Placenta	Placenta
45	chr1:85741800-85743000	Active TSS	HSMMtube	muscle
46	chr1:85741800-85743200	Active TSS	Brain Substantia Nigra	brain
47	chr1:85741800-85743400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:85742000-85743000	Active TSS	Brain Germinal Matrix	brain
49	chr1:85742000-85743000	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr1:85742200-85743000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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