Variant report

Variant	rs12060797
Chromosome Location	chr1:150206253-150206254
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	FOXA1	chr1:150206237-150206518	HepG2	liver:	n/a	chr1:150206383-150206398
2	SPI1	chr1:150205966-150206519	HL-60	blood:	n/a	n/a
3	STAT5A	chr1:150206218-150209018	GM12878	blood:	n/a	chr1:150206545-150206557 chr1:150206734-150206746
4	NFATC1	chr1:150206073-150207549	GM12878	blood:	n/a	n/a
5	FOXA2	chr1:150206186-150206577	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:150205972-150209097	HL-60	blood:	n/a	n/a
7	NR2F2	chr1:150205918-150206700	MCF-7	breast:	n/a	n/a
8	TEAD4	chr1:150205998-150207537	K562	blood:	n/a	n/a
9	SIN3AK20	chr1:150205702-150209385	MCF-7	breast:	n/a	n/a
10	CEBPB	chr1:150206210-150206738	A549	lung:	n/a	n/a
11	POLR2A	chr1:150205956-150209660	GM12891	blood:	n/a	n/a
12	HDAC2	chr1:150205952-150209231	MCF-7	breast:	n/a	chr1:150206648-150206662 chr1:150208282-150208296 chr1:150206647-150206661 chr1:150206644-150206658
13	ZNF384	chr1:150206167-150207262	GM12878	blood:	n/a	n/a
14	WRNIP1	chr1:150205802-150206261	GM12878	blood:	n/a	n/a
15	FOXA1	chr1:150206166-150206548	T-47D	breast:	n/a	chr1:150206383-150206398
16	BCL3	chr1:150206122-150207237	A549	lung:	n/a	chr1:150207027-150207036 chr1:150206979-150206992
17	RELA	chr1:150205988-150209001	GM12891	blood:	n/a	n/a
18	POLR2A	chr1:150205839-150209223	HL-60	blood:	n/a	n/a
19	MAZ	chr1:150205735-150209200	IMR90	lung:	n/a	chr1:150208066-150208075 chr1:150206549-150206559 chr1:150207801-150207811 chr1:150207729-150207738
20	FOXA2	chr1:150205983-150206881	HepG2	liver:	n/a	n/a
21	PML	chr1:150206208-150207704	K562	blood:	n/a	n/a
22	POLR2A	chr1:150206158-150209657	GM12878	blood:	n/a	n/a
23	SP1	chr1:150206007-150207558	A549	lung:	n/a	chr1:150206548-150206557 chr1:150206544-150206558 chr1:150206547-150206559 chr1:150207041-150207050 chr1:150207039-150207051 chr1:150206553-150206565 chr1:150207041-150207050 chr1:150207201-150207212 chr1:150207040-150207049 chr1:150206554-150206563 chr1:150207187-150207196 chr1:150207186-150207197
24	RELA	chr1:150206035-150207564	GM10847	blood:	n/a	n/a
25	MAZ	chr1:150206162-150209060	K562	blood:	n/a	chr1:150208066-150208075 chr1:150206549-150206559 chr1:150207801-150207811 chr1:150207729-150207738
26	FOXA1	chr1:150206088-150206590	HepG2	liver:	n/a	chr1:150206383-150206398
27	POLR2A	chr1:150205935-150209076	GM12878	blood:	n/a	n/a
28	FOXA2	chr1:150206169-150206767	A549	lung:	n/a	n/a
29	SP1	chr1:150205913-150207386	A549	lung:	n/a	chr1:150206548-150206557 chr1:150206544-150206558 chr1:150206547-150206559 chr1:150207041-150207050 chr1:150207039-150207051 chr1:150206553-150206565 chr1:150207041-150207050 chr1:150207201-150207212 chr1:150207040-150207049 chr1:150206554-150206563 chr1:150207187-150207196 chr1:150207186-150207197
30	POLR2A	chr1:150205850-150209137	GM12878	blood:	n/a	n/a
31	UBTF	chr1:150206222-150206480	K562	blood:	n/a	n/a
32	BRCA1	chr1:150206166-150207287	Hela-S3	cervix:	n/a	n/a
33	EP300	chr1:150206093-150206698	A549	lung:	n/a	n/a
34	CEBPB	chr1:150205871-150206639	A549	lung:	n/a	chr1:150206049-150206060
35	POLR2A	chr1:150206119-150206504	GM12878	blood:	n/a	n/a
36	MTA3	chr1:150205645-150209670	GM12878	blood:	n/a	n/a
37	CHD1	chr1:150205602-150209284	IMR90	lung:	n/a	chr1:150206544-150206554 chr1:150207090-150207100
38	CHD1	chr1:150206002-150209049	GM12878	blood:	n/a	chr1:150206544-150206554 chr1:150207090-150207100
39	CEBPB	chr1:150205855-150207412	Hela-S3	cervix:	n/a	chr1:150206049-150206060
40	USF2	chr1:150206068-150206264	GM12878	blood:	n/a	n/a
41	E2F4	chr1:150206038-150207386	MCF10A-Er-Src	breast:	n/a	chr1:150206548-150206557
42	NFIC	chr1:150206073-150209104	GM12878	blood:	n/a	chr1:150206737-150206765 chr1:150208613-150208629
43	EP300	chr1:150206058-150206664	A549	lung:	n/a	n/a
44	CUX1	chr1:150206187-150207368	GM12878	blood:	n/a	chr1:150206889-150206898
45	SIN3AK20	chr1:150205694-150207458	MCF-7	breast:	n/a	n/a
46	FOXA1	chr1:150206147-150206655	HepG2	liver:	n/a	chr1:150206383-150206398
47	TCF12	chr1:150205971-150209189	A549	lung:	n/a	n/a
48	FOXA2	chr1:150206197-150206771	A549	lung:	n/a	n/a
49	CEBPB	chr1:150206031-150206679	MCF-7	breast:	n/a	chr1:150206049-150206060
50	REST	chr1:150206036-150207479	A549	lung:	n/a	chr1:150206733-150206746

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:150206242-150206292	AG09309	skin:	n/a
2	chr1:150206242-150206292	NT2-D1	testis:	n/a
3	chr1:150206242-150206292	SK-N-SH_RA	brain:	n/a
4	chr1:150206242-150206292	HRE	kidney:	n/a
5	chr1:150206242-150206292	HL-60	blood:	n/a
6	chr1:150206242-150206292	HCF	heart:	n/a
7	chr1:150206242-150206292	SKMC	muscle:	n/a
8	chr1:150206242-150206292	SK-N-MC	brain:	n/a
9	chr1:150206242-150206292	GM19239	blood:	n/a
10	chr1:150206242-150206292	HCM	heart:	n/a
11	chr1:150206242-150206292	NHBE	bronchial:	n/a
12	chr1:150206242-150206292	HNPCEpiC	eye:	n/a
13	chr1:150206242-150206292	Hela-S3	cervix:	n/a
14	chr1:150206242-150206292	AoSMC	blood vessel:	n/a
15	chr1:150206242-150206292	HRCEpiC	kidney:	n/a
16	chr1:150206242-150206292	LNCaP	prostate:	n/a
17	chr1:150206242-150206292	NH-A	brain:	n/a
18	chr1:150206242-150206292	SK-N-SH	brain:	n/a
19	chr1:150206242-150206292	HPAEpiC	pulmonary alveolar:	n/a
20	chr1:150206242-150206292	MCF-7	breast:	n/a
21	chr1:150206242-150206292	HCPEpiC	choroid plexus:	n/a
22	chr1:150206242-150206292	Hepatocyte	liver:	n/a
23	chr1:150206242-150206292	HIPEpiC	eye:	n/a
24	chr1:150206242-150206292	RPTEC	kidney:	n/a
25	chr1:150206242-150206292	H1-hESC	embryonic stem cell:	embryo
26	chr1:150206242-150206292	Jurkat	blood:	n/a
27	chr1:150206242-150206292	GM12891	blood:	n/a
28	chr1:150206242-150206292	HCT-116	colon:	n/a
29	chr1:150206242-150206292	K562	blood:	n/a
30	chr1:150206242-150206292	SAEC	small airway:	n/a
31	chr1:150206242-150206292	HUVEC	blood vessel:	n/a
32	chr1:150206242-150206292	GM12878	blood:	n/a
33	chr1:150206242-150206292	PANC-1	pancreas:	n/a
34	chr1:150206242-150206292	NHDF-neo	bronchial:	n/a
35	chr1:150206242-150206292	PFSK-1	brain:	n/a
36	chr1:150206242-150206292	HAEpiC	amniotic membrane:	n/a
37	chr1:150206242-150206292	BJ	skin:	n/a
38	chr1:150206242-150206292	HEK293	kidney:	embryo
39	chr1:150206242-150206292	BE2_C	brain:	n/a
40	chr1:150206242-150206292	U87	brain:	n/a
41	chr1:150206242-150206292	AG04449	skin:	fetal
42	chr1:150206242-150206292	ovcar-3	ovarian:	n/a
43	chr1:150206242-150206292	MCF10A-Er-Src	breast:	n/a
44	chr1:150206242-150206292	ProgFib	skin:	n/a
45	chr1:150206242-150206292	CMK	blood:	n/a
46	chr1:150206242-150206292	AG04450	lung:	fetal
47	chr1:150206242-150206292	HEEpiC	esophagus:	n/a
48	chr1:150206242-150206292	ECC-1	luminal epithelium:	n/a
49	chr1:150206242-150206292	HRPEpiC	eye:	n/a
50	chr1:150206242-150206292	A549	lung:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150206253..150206969-chr17:71227981..71228545,2	Hela-S3	cervix:
2	chr1:149980534..149984301-chr1:150205783..150209955,5	K562	blood:
3	chr1:150206170..150208675-chr1:150264452..150269195,6	MCF-7	breast:
4	chr1:150203436..150211066-chr1:150333611..150339492,20	K562	blood:
5	chr1:149870500..149872892-chr1:150205749..150208479,2	MCF-7	breast:
6	chr1:150205674..150207849-chr1:150521366..150523683,3	K562	blood:
7	chr1:150193027..150195228-chr1:150205376..150206988,2	MCF-7	breast:
8	chr1:150205825..150209635-chr1:150259375..150267858,10	K562	blood:
9	chr1:150206250..150210524-chr1:150335148..150338813,9	MCF-7	breast:
10	chr1:150205879..150210456-chr1:150251557..150256195,8	MCF-7	breast:
11	chr1:150204090..150209498-chr1:150239337..150243073,9	K562	blood:
12	chr1:150120783..150123550-chr1:150205612..150208208,2	K562	blood:
13	chr1:150175161..150177546-chr1:150204659..150206770,2	K562	blood:
14	chr1:149857691..149860946-chr1:150205716..150209343,6	MCF-7	breast:
15	chr1:150196400..150199803-chr1:150204196..150206419,3	K562	blood:
16	chr1:150205006..150208304-chr1:150532619..150536152,3	MCF-7	breast:
17	chr1:150205585..150207162-chr1:150228414..150230615,2	K562	blood:
18	chr1:150198495..150205043-chr1:150206226..150211170,11	MCF-7	breast:
19	chr1:150205150..150208917-chr1:150946080..150950396,4	MCF-7	breast:
20	chr1:150205585..150209843-chr1:150227901..150231226,5	K562	blood:
21	chr1:150204882..150207260-chr1:150266148..150269015,2	MCF-7	breast:
22	chr1:150205053..150211036-chr1:150333116..150338498,15	K562	blood:
23	chr1:150182307..150185860-chr1:150205787..150209000,3	K562	blood:

Variant related genes	Relation type
RNU2-17P	TF binding region
RNU2-17P	CpG island
ENSG00000178096	Chromatin interaction
ENSG00000271845	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000187145	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000118292	Chromatin interaction
ENSG00000141219	Chromatin interaction
ENSG00000118298	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000225996	Chromatin interaction
ENSG00000117362	Chromatin interaction
ENSG00000163113	Chromatin interaction
ENSG00000159208	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000266187	Chromatin interaction
ENSG00000133193	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000143382	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11205344	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12057743	0.87[AFR][1000 genomes]
rs12063159	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12075620	0.89[AMR][1000 genomes]
rs13375906	0.89[AMR][1000 genomes]
rs3121003	0.89[AMR][1000 genomes]
rs73009573	0.89[AMR][1000 genomes]
rs73009583	0.89[AMR][1000 genomes]
rs73009584	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 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	chr1:150184200-150206600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:150186200-150206800	Weak transcription	Spleen	Spleen
3	chr1:150186400-150206800	Weak transcription	Esophagus	oesophagus
4	chr1:150186600-150206400	Weak transcription	Aorta	Aorta
5	chr1:150186800-150206800	Weak transcription	Pancreas	Pancrea
6	chr1:150192800-150206800	Weak transcription	Gastric	stomach
7	chr1:150198200-150206600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:150199200-150206400	Weak transcription	Ovary	ovary
9	chr1:150200000-150206800	Weak transcription	Lung	lung
10	chr1:150201000-150206800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:150202200-150206800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:150203800-150206400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:150205000-150206400	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:150205000-150208800	Active TSS	GM12878-XiMat	blood
15	chr1:150205200-150206400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:150205400-150206600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:150205600-150206400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:150205600-150206400	Flanking Active TSS	K562	blood
19	chr1:150205600-150206600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:150205600-150206600	Flanking Active TSS	Hela-S3	cervix
21	chr1:150205600-150206600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr1:150205800-150206400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr1:150205800-150206400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr1:150205800-150206400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:150205800-150206400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:150205800-150206400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr1:150205800-150206400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr1:150205800-150206400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:150205800-150206400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:150205800-150206400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:150205800-150206400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:150205800-150206400	Enhancers	Brain Cingulate Gyrus	brain
33	chr1:150205800-150206400	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr1:150205800-150206400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr1:150205800-150206400	Flanking Active TSS	A549	lung
36	chr1:150205800-150206400	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr1:150205800-150206400	Flanking Active TSS	NH-A	brain
38	chr1:150205800-150206400	Flanking Active TSS	NHDF-Ad	bronchial
39	chr1:150205800-150206400	Flanking Active TSS	Osteobl	bone
40	chr1:150205800-150206600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr1:150205800-150206600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:150205800-150206600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr1:150205800-150206600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr1:150205800-150206600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:150205800-150206600	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr1:150205800-150206800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr1:150205800-150206800	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr1:150205800-150206800	Flanking Active TSS	Fetal Thymus	thymus
49	chr1:150205800-150207000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr1:150205800-150207000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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