Variant report

Variant	rs12068788
Chromosome Location	chr1:85741734-85741735
allele	A/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	FOXM1	chr1:85741329-85741796	GM12878	blood:	n/a	n/a
2	BRCA1	chr1:85741421-85741879	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:85741401-85742816	HepG2	liver:	n/a	n/a
4	SRF	chr1:85741461-85743025	HCT-116	colon:	n/a	n/a
5	POLR2A	chr1:85741574-85742850	ProgFib	skin:	n/a	n/a
6	TAF1	chr1:85741634-85742811	ECC-1	luminal epithelium:	n/a	n/a
7	TAF1	chr1:85741693-85742708	HepG2	liver:	n/a	n/a
8	NFIC	chr1:85741629-85742189	GM12878	blood:	n/a	n/a
9	GABPA	chr1:85741710-85742733	A549	lung:	n/a	chr1:85741945-85741954 chr1:85741911-85741918
10	STAT1	chr1:85741632-85742729	GM12878	blood:	n/a	n/a
11	RAD21	chr1:85741588-85742394	IMR90	lung:	n/a	chr1:85742287-85742296
12	POLR2A	chr1:85741719-85742814	K562	blood:	n/a	n/a
13	GABPA	chr1:85741658-85742949	SK-N-SH	brain:	n/a	chr1:85741945-85741954 chr1:85741911-85741918
14	POLR2A	chr1:85741694-85742784	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:85740468-85743570	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr1:85740591-85742964	GM12891	blood:	n/a	n/a
17	ZNF143	chr1:85741679-85742630	H1-hESC	embryonic stem cell:	n/a	chr1:85741944-85741954
18	POLR2A	chr1:85741655-85742724	K562	blood:	n/a	n/a
19	PML	chr1:85741383-85741751	GM12878	blood:	n/a	n/a
20	SIN3AK20	chr1:85741227-85742279	PANC-1	pancreas:	n/a	n/a
21	ELF1	chr1:85741703-85742743	K562	blood:	n/a	chr1:85742651-85742662 chr1:85742210-85742219 chr1:85742209-85742222 chr1:85742343-85742355
22	ELF1	chr1:85741515-85742975	HCT-116	colon:	n/a	chr1:85742651-85742662 chr1:85742210-85742219 chr1:85742209-85742222 chr1:85742343-85742355
23	NFIC	chr1:85741649-85742180	ECC-1	luminal epithelium:	n/a	n/a
24	TAF1	chr1:85741434-85742652	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr1:85741665-85742849	NB4	blood:	n/a	chr1:85741944-85741954
26	KAP1	chr1:85740518-85742974	HEK293	kidney:	n/a	chr1:85741050-85741059
27	RELA	chr1:85740582-85742917	GM12878	blood:	n/a	chr1:85741485-85741494 chr1:85741485-85741494
28	POLR2A	chr1:85741210-85742785	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:85741369-85742939	Raji	blood:	n/a	n/a
30	MTA3	chr1:85741236-85742914	GM12878	blood:	n/a	n/a
31	HEY1	chr1:85741619-85742871	HepG2	liver:	n/a	chr1:85741928-85741943 chr1:85742088-85742103 chr1:85742080-85742095
32	MYC	chr1:85741486-85742880	NB4	blood:	n/a	chr1:85741944-85741954
33	ELK4	chr1:85741271-85742801	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr1:85740603-85742874	K562	blood:	n/a	n/a
35	POU2F2	chr1:85741323-85741849	GM12891	blood:	n/a	chr1:85741534-85741542 chr1:85741534-85741544
36	POLR2A	chr1:85741694-85742798	K562	blood:	n/a	n/a
37	POLR2A	chr1:85741287-85742805	GM12891	blood:	n/a	n/a
38	CREB1	chr1:85741595-85742788	K562	blood:	n/a	n/a
39	CHD1	chr1:85740696-85742142	GM12878	blood:	n/a	n/a
40	HCFC1	chr1:85740700-85743065	Hela-S3	cervix:	n/a	n/a
41	SPI1	chr1:85741670-85742802	HL-60	blood:	n/a	chr1:85741908-85741921
42	POLR2A	chr1:85741682-85742910	U87	brain:	n/a	n/a
43	RCOR1	chr1:85741701-85742808	Hela-S3	cervix:	n/a	n/a
44	MTA3	chr1:85741241-85742169	GM12878	blood:	n/a	n/a
45	RELA	chr1:85740690-85742803	GM19099	blood:	n/a	chr1:85741485-85741494 chr1:85741485-85741494
46	POLR2A	chr1:85740638-85742911	GM12878	blood:	n/a	n/a
47	RELA	chr1:85740946-85741847	GM10847	blood:	n/a	chr1:85741485-85741494 chr1:85741485-85741494
48	POLR2A	chr1:85741721-85742744	K562	blood:	n/a	n/a
49	CREB1	chr1:85741729-85742871	HepG2	liver:	n/a	n/a
50	POLR2A	chr1:85741656-85742806	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85739753..85743262-chr1:86045535..86049012,3	K562	blood:
2	chr1:85665913..85668656-chr1:85741362..85743092,3	MCF-7	breast:
3	chr1:85665631..85669772-chr1:85739485..85744059,5	K562	blood:
4	chr1:85740297..85741951-chr1:85930278..85931798,2	MCF-7	breast:
5	chr1:85740856..85742558-chr1:86046586..86048600,2	MCF-7	breast:
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	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:

Variant related genes	Relation type
ENSG00000223653	TF binding region
ENSG00000272691	Chromatin interaction
ENSG00000153904	Chromatin interaction
ENSG00000097096	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161564	0.93[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs11161581	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11161583	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12065528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12066982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12068389	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12084232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12086970	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12087340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12562182	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12563515	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12726649	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12743302	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12744565	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12746169	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17124345	0.93[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs35486093	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35783363	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35798604	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs36116171	0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4074156	0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4258258	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6693229	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9887811	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9887812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9887879	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:127 , 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	chr1:85739600-85741800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr1:85739600-85742200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:85739800-85741800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:85739800-85742800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:85740000-85741800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr1:85740200-85741800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr1:85740200-85743200	Active TSS	Colonic Mucosa	Colon
9	chr1:85740400-85741800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr1:85740400-85742400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:85740400-85742600	Active TSS	GM12878-XiMat	blood
12	chr1:85740400-85742800	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr1:85740600-85741800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:85740600-85741800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr1:85740600-85741800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr1:85740600-85741800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:85740600-85741800	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:85740600-85741800	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr1:85740600-85741800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:85740600-85742000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr1:85740600-85742800	Active TSS	Fetal Intestine Large	intestine
22	chr1:85740600-85742800	Active TSS	Ovary	ovary
23	chr1:85740600-85743000	Active TSS	Right Atrium	heart
24	chr1:85740600-85743000	Active TSS	Right Ventricle	heart
25	chr1:85740600-85743200	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr1:85740600-85743200	Active TSS	Esophagus	oesophagus
27	chr1:85740800-85741800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr1:85740800-85741800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr1:85740800-85741800	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr1:85740800-85741800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr1:85740800-85741800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:85740800-85741800	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr1:85740800-85742200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:85740800-85742600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:85740800-85742600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr1:85740800-85742600	Active TSS	HMEC	breast
37	chr1:85740800-85742600	Active TSS	NHEK	skin
38	chr1:85740800-85742800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:85740800-85742800	Active TSS	Left Ventricle	heart
40	chr1:85740800-85742800	Active TSS	Stomach Mucosa	stomach
41	chr1:85740800-85742800	Active TSS	NHDF-Ad	bronchial
42	chr1:85740800-85742800	Active TSS	NHLF	lung
43	chr1:85740800-85743000	Active TSS	Aorta	Aorta
44	chr1:85740800-85743400	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr1:85741000-85741800	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr1:85741000-85741800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr1:85741000-85741800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr1:85741000-85742600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr1:85741000-85742600	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr1:85741000-85742600	Active TSS	NH-A	brain

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