Variant report

Variant	rs12406712
Chromosome Location	chr1:150545084-150545085
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:103)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HMGN3	chr1:150544959-150545129	K562	blood:	n/a	n/a
2	POLR2A	chr1:150543194-150546558	HepG2	liver:	n/a	n/a
3	MTA3	chr1:150544950-150546278	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:150544888-150545324	HL-60	blood:	n/a	n/a
5	CCNT2	chr1:150544950-150545145	K562	blood:	n/a	chr1:150545121-150545130
6	POLR2A	chr1:150538698-150546656	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:150544288-150546564	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:150538889-150552727	K562	blood:	n/a	n/a
9	POLR2A	chr1:150538866-150546573	U87	brain:	n/a	n/a
10	POLR2A	chr1:150539774-150546448	HUVEC	blood vessel:	n/a	n/a
11	FOS	chr1:150544783-150545121	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr1:150545018-150545397	GM12891	blood:	n/a	n/a
13	CHD2	chr1:150544925-150546197	K562	blood:	n/a	n/a
14	POLR2A	chr1:150541963-150546408	HUVEC	blood vessel:	n/a	n/a
15	TEAD4	chr1:150544936-150546577	K562	blood:	n/a	n/a
16	POLR2A	chr1:150543224-150546653	K562	blood:	n/a	n/a
17	ATF2	chr1:150544357-150545087	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:150527732-150552686	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr1:150544393-150545359	HCT-116	colon:	n/a	n/a
20	SIN3AK20	chr1:150543601-150546543	K562	blood:	n/a	n/a
21	POLR2A	chr1:150530622-150553130	IMR90	lung:	n/a	n/a
22	POLR2A	chr1:150544897-150545171	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:150540216-150546538	U87	brain:	n/a	n/a
24	POLR2A	chr1:150544471-150546444	GM12892	blood:	n/a	n/a
25	POLR2A	chr1:150538654-150552953	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:150544267-150545162	ProgFib	skin:	n/a	n/a
27	POLR2A	chr1:150544818-150546306	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr1:150543314-150546680	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr1:150539727-150546572	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:150530539-150552850	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr1:150538736-150552926	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:150538866-150553173	U87	brain:	n/a	n/a
33	POLR2A	chr1:150538945-150546560	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr1:150544980-150546467	K562	blood:	n/a	n/a
35	POLR2A	chr1:150542302-150546578	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr1:150538877-150553278	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:150538822-150553196	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr1:150542706-150546537	K562	blood:	n/a	n/a
39	POLR2A	chr1:150543438-150546395	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr1:150544939-150546549	HepG2	liver:	n/a	n/a
41	POLR2A	chr1:150542040-150546487	GM12891	blood:	n/a	n/a
42	POLR2A	chr1:150541942-150546679	GM12891	blood:	n/a	n/a
43	POLR2A	chr1:150541930-150546677	GM12891	blood:	n/a	n/a
44	POLR2A	chr1:150543208-150546659	GM12891	blood:	n/a	n/a
45	POLR2A	chr1:150544947-150545108	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:150538740-150553070	K562	blood:	n/a	n/a
47	POLR2A	chr1:150538874-150549135	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:150544830-150545163	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:150543394-150546610	GM19193	blood:	n/a	n/a
50	POLR2A	chr1:150538937-150546714	GM12892	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150258806..150260952-chr1:150544503..150546807,2	K562	blood:
2	chr1:150455770..150459652-chr1:150544183..150547234,4	K562	blood:
3	chr1:150543953..150547860-chr1:150600449..150605575,7	K562	blood:
4	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
5	chr1:150543938..150548482-chr1:150576509..150579510,5	K562	blood:
6	chr1:150543642..150545689-chr1:150586263..150588774,2	MCF-7	breast:
7	chr1:150544693..150547632-chr1:150583989..150587707,3	MCF-7	breast:
8	chr1:150544010..150546916-chr1:150590925..150592477,2	MCF-7	breast:
9	chr1:150543916..150546115-chr1:150744599..150746718,2	K562	blood:
10	chr1:150542528..150547161-chr1:150576124..150579510,4	K562	blood:
11	chr1:150455770..150457599-chr1:150544025..150546783,3	K562	blood:
12	chr1:150542997..150546031-chr1:150978720..150981188,4	MCF-7	breast:
13	chr1:150435919..150438376-chr1:150544338..150547064,3	K562	blood:

No data

Variant related genes	Relation type
RN7SL600P	TF binding region
ENSG00000143420	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000143409	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1053732	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10888384	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10888385	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11204668	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204669	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11204675	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11204677	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204678	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11204679	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11204680	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11204684	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11585169	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12116492	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12125672	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126271	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12139563	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12746899	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1971378	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2048558	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3738484	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3738485	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754209	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4970918	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4970923	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4971041	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55862611	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820165	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669122	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6697620	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6698495	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs878471	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs932054	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9803935	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12406712	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs12406712	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs12406712	HORMAD1	cis	Esophagus Mucosa	GTEx
rs12406712	HORMAD1	cis	Nerve Tibial	GTEx
rs12406712	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs12406712	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs12406712	GOLPH3L	cis	Nerve Tibial	GTEx
rs12406712	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs12406712	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs12406712	ARNT	cis	Thyroid	GTEx
rs12406712	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs12406712	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150534400-150547200	Weak transcription	Ovary	ovary
2	chr1:150540800-150545600	Enhancers	Right Atrium	heart
3	chr1:150540800-150545600	Enhancers	Right Ventricle	heart
4	chr1:150541400-150545400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:150541400-150545600	Genic enhancers	Rectal Mucosa Donor 31	rectum
6	chr1:150541400-150545800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:150541400-150547200	Genic enhancers	Fetal Intestine Small	intestine
8	chr1:150541400-150549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:150541600-150545200	Weak transcription	Fetal Kidney	kidney
10	chr1:150541600-150545600	Weak transcription	Brain Angular Gyrus	brain
11	chr1:150541800-150546800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:150542000-150545400	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr1:150542000-150545600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:150542000-150545600	Strong transcription	Fetal Brain Female	brain
15	chr1:150542000-150547200	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:150542200-150545200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:150542200-150545600	Genic enhancers	Rectal Mucosa Donor 29	rectum
18	chr1:150542200-150547200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:150542200-150547200	Strong transcription	Brain Germinal Matrix	brain
20	chr1:150542200-150548000	Genic enhancers	Placenta	Placenta
21	chr1:150542400-150545600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:150542400-150546800	Genic enhancers	Fetal Muscle Leg	muscle
23	chr1:150542400-150547000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:150542600-150545200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:150542600-150545400	Weak transcription	Brain Substantia Nigra	brain
26	chr1:150542600-150545600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:150542600-150545600	Genic enhancers	Adipose Nuclei	Adipose
28	chr1:150542600-150545600	Genic enhancers	Liver	Liver
29	chr1:150542600-150545600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:150542600-150547200	Genic enhancers	Lung	lung
31	chr1:150542600-150548200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:150542800-150545200	Weak transcription	Hela-S3	cervix
33	chr1:150542800-150545200	Weak transcription	HepG2	liver
34	chr1:150542800-150545200	Weak transcription	K562	blood
35	chr1:150542800-150545400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:150542800-150545400	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr1:150542800-150545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:150542800-150545800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:150542800-150547800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:150542800-150551600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
41	chr1:150543000-150545200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:150543000-150546000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:150543000-150549200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:150543200-150545200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:150543200-150545200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:150543200-150545200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:150543200-150545400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:150543200-150545600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:150543200-150545800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:150543200-150547000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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