Variant report

Variant	rs1706476
Chromosome Location	chr12:123921349-123921350
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	POLR2A	chr12:123920837-123921446	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:123918547-123921691	GM12878	blood:	n/a	n/a
3	CEBPB	chr12:123920936-123921419	HepG2	liver:	n/a	chr12:123921108-123921119 chr12:123921107-123921120
4	POLR2A	chr12:123920960-123921463	K562	blood:	n/a	n/a
5	HEY1	chr12:123920782-123921453	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:123920722-123921351	GM12891	blood:	n/a	n/a
7	POLR2A	chr12:123920585-123921698	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:123920781-123921392	GM12892	blood:	n/a	n/a
9	MAZ	chr12:123921010-123921634	Hela-S3	cervix:	n/a	n/a
10	TAF1	chr12:123921006-123921411	K562	blood:	n/a	n/a
11	ATF2	chr12:123920737-123921522	GM12878	blood:	n/a	n/a
12	NRF1	chr12:123920968-123921468	GM12878	blood:	n/a	chr12:123921123-123921132
13	IRF4	chr12:123920999-123921457	GM12878	blood:	n/a	n/a
14	ZBTB7A	chr12:123920501-123921367	ECC-1	luminal epithelium:	n/a	n/a
15	CEBPB	chr12:123920906-123921535	MCF-7	breast:	n/a	chr12:123921108-123921119 chr12:123921107-123921120
16	POLR2A	chr12:123920485-123921402	GM12892	blood:	n/a	n/a
17	CTCF	chr12:123921300-123921450	HUVEC	blood vessel:	n/a	chr12:123921344-123921357
18	POLR2A	chr12:123920488-123921357	GM12891	blood:	n/a	n/a
19	YY1	chr12:123920984-123921384	K562	blood:	n/a	n/a
20	CCNT2	chr12:123920491-123921476	K562	blood:	n/a	chr12:123921326-123921335
21	GTF2F1	chr12:123921232-123921455	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr12:123920648-123921768	ECC-1	luminal epithelium:	n/a	n/a
23	MTA3	chr12:123920773-123921638	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:123920886-123921488	Hela-S3	cervix:	n/a	n/a
25	RFX5	chr12:123921085-123921405	HepG2	liver:	n/a	chr12:123921357-123921372
26	PML	chr12:123920961-123921425	K562	blood:	n/a	n/a
27	E2F4	chr12:123921237-123921423	MCF10A-Er-Src	breast:	n/a	n/a
28	BCL11A	chr12:123920983-123921362	GM12878	blood:	n/a	chr12:123921158-123921171 chr12:123921162-123921175
29	CTCF	chr12:123921220-123921370	HBMEC	blood vessel:	n/a	chr12:123921344-123921357
30	EP300	chr12:123921347-123921590	K562	blood:	n/a	chr12:123921527-123921543
31	POLR2A	chr12:123920543-123921633	GM18526	blood:	n/a	n/a
32	POLR2A	chr12:123919909-123921875	HL-60	blood:	n/a	n/a
33	TBP	chr12:123920990-123921539	GM12878	blood:	n/a	n/a
34	CTCF	chr12:123921240-123921390	GM12875	blood:	n/a	chr12:123921344-123921357
35	RAD21	chr12:123921246-123921451	Hela-S3	cervix:	n/a	chr12:123921343-123921356 chr12:123921299-123921312
36	CTCF	chr12:123921260-123921410	HepG2	liver:	n/a	chr12:123921344-123921357
37	RCOR1	chr12:123921053-123921840	Hela-S3	cervix:	n/a	n/a
38	KAP1	chr12:123921301-123921771	K562	blood:	n/a	chr12:123921481-123921489
39	POU2F2	chr12:123920862-123921550	GM12878	blood:	n/a	chr12:123921453-123921460
40	CREB1	chr12:123920533-123921664	GM12878	blood:	n/a	n/a
41	USF2	chr12:123920929-123921619	GM12878	blood:	n/a	chr12:123921531-123921547
42	UBTF	chr12:123921012-123921489	K562	blood:	n/a	n/a
43	MAX	chr12:123920910-123921485	H1-hESC	embryonic stem cell:	n/a	n/a
44	ETS1	chr12:123920977-123921418	GM12878	blood:	n/a	chr12:123921026-123921033 chr12:123921194-123921205 chr12:123921193-123921207
45	MAX	chr12:123920544-123921525	GM12878	blood:	n/a	n/a
46	SP1	chr12:123920791-123921581	A549	lung:	n/a	chr12:123921326-123921335 chr12:123921325-123921335 chr12:123921324-123921336 chr12:123921325-123921334 chr12:123921325-123921334 chr12:123921324-123921336 chr12:123921325-123921335
47	ETS1	chr12:123920860-123921434	GM12878	blood:	n/a	chr12:123921026-123921033 chr12:123921194-123921205 chr12:123921193-123921207
48	RCOR1	chr12:123920624-123921938	K562	blood:	n/a	n/a
49	ELF1	chr12:123920861-123921512	K562	blood:	n/a	n/a
50	MAX	chr12:123920604-123921912	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:123921306-123921356	H1-hESC	embryonic stem cell:	embryo
2	chr12:123921306-123921356	NB4	blood:	n/a
3	chr12:123921306-123921356	CMK	blood:	n/a
4	chr12:123921306-123921356	PFSK-1	brain:	n/a
5	chr12:123921306-123921356	ProgFib	skin:	n/a
6	chr12:123921306-123921356	MCF-7	breast:	n/a
7	chr12:123921306-123921356	HCPEpiC	choroid plexus:	n/a
8	chr12:123921306-123921356	K562	blood:	n/a
9	chr12:123921306-123921356	SAEC	small airway:	n/a
10	chr12:123921306-123921356	NH-A	brain:	n/a
11	chr12:123921306-123921356	HUVEC	blood vessel:	n/a
12	chr12:123921306-123921356	HAEpiC	amniotic membrane:	n/a
13	chr12:123921306-123921356	IMR90	lung:	fetal
14	chr12:123921306-123921356	AoSMC	blood vessel:	n/a
15	chr12:123921306-123921356	AG04449	skin:	fetal
16	chr12:123921306-123921356	HPAEpiC	pulmonary alveolar:	n/a
17	chr12:123921306-123921356	GM12891	blood:	n/a
18	chr12:123921306-123921356	AG09309	skin:	n/a
19	chr12:123921306-123921356	NHDF-neo	bronchial:	n/a
20	chr12:123921306-123921356	U87	brain:	n/a
21	chr12:123921306-123921356	BE2_C	brain:	n/a
22	chr12:123921306-123921356	ovcar-3	ovarian:	n/a
23	chr12:123921306-123921356	Hela-S3	cervix:	n/a
24	chr12:123921306-123921356	AG04450	lung:	fetal
25	chr12:123921306-123921356	GM19239	blood:	n/a
26	chr12:123921306-123921356	GM12892	blood:	n/a
27	chr12:123921306-123921356	GM06990	blood:	n/a
28	chr12:123921306-123921356	SK-N-SH	brain:	n/a
29	chr12:123921306-123921356	HL-60	blood:	n/a
30	chr12:123921306-123921356	Caco-2	colon:	n/a
31	chr12:123921306-123921356	HMEC	breast:	n/a
32	chr12:123921306-123921356	PANC-1	pancreas:	n/a
33	chr12:123921306-123921356	AG09319	gingival:	n/a
34	chr12:123921306-123921356	AG10803	skin:	n/a
35	chr12:123921306-123921356	NHBE	bronchial:	n/a
36	chr12:123921306-123921356	HRE	kidney:	n/a
37	chr12:123921306-123921356	NT2-D1	testis:	n/a
38	chr12:123921306-123921356	HRPEpiC	eye:	n/a
39	chr12:123921306-123921356	HCT-116	colon:	n/a
40	chr12:123921306-123921356	SKMC	muscle:	n/a
41	chr12:123921306-123921356	RPTEC	kidney:	n/a
42	chr12:123921306-123921356	Hepatocyte	liver:	n/a
43	chr12:123921306-123921356	SK-N-MC	brain:	n/a
44	chr12:123921306-123921356	MCF10A-Er-Src	breast:	n/a
45	chr12:123921306-123921356	A549	lung:	n/a
46	chr12:123921306-123921356	BJ	skin:	n/a
47	chr12:123921306-123921356	SK-N-SH_RA	brain:	n/a
48	chr12:123921306-123921356	LNCaP	prostate:	n/a
49	chr12:123921306-123921356	T-47D	breast:	n/a
50	chr12:123921306-123921356	PrEC	prostate:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123921165..123922728-chr12:124019054..124020967,2	K562	blood:
2	chr11:62572551..62573135-chr12:123920915..123921735,2	Hela-S3	cervix:
3	chr12:123866820..123869752-chr12:123919792..123923261,3	K562	blood:
4	chr12:123919998..123924322-chr12:123941781..123944675,4	K562	blood:
5	chr12:123919731..123922838-chr12:123939726..123943639,4	MCF-7	breast:
6	chr12:123872355..123875545-chr12:123919640..123922793,3	MCF-7	breast:
7	chr12:123919342..123922431-chr12:123924734..123927863,4	MCF-7	breast:
8	chr12:123920837..123922890-chr12:124067881..124069805,2	K562	blood:

Variant related genes	Relation type
RILPL2	TF binding region
RILPL2	CpG island
ENSG00000247373	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000270445	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000266655	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11507736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11507738	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1706475	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961025	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs871163	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers 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	48 gene(s)	inside rSNPs	diseases
4	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1706476	MGC7036	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123917200-123921800	Active TSS	Aorta	Aorta
2	chr12:123918600-123921400	Active TSS	GM12878-XiMat	blood
3	chr12:123918800-123921600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:123919800-123921800	Active TSS	Fetal Kidney	kidney
5	chr12:123920000-123921400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:123920000-123921600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:123920000-123921600	Active TSS	Ovary	ovary
8	chr12:123920000-123921800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:123920000-123921800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:123920000-123921800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:123920000-123921800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr12:123920000-123921800	Active TSS	HSMM	muscle
13	chr12:123920000-123921800	Active TSS	NHLF	lung
14	chr12:123920200-123921400	Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr12:123920200-123921400	Active TSS	Monocytes-CD14+_RO01746	blood
16	chr12:123920200-123921600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:123920200-123921600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:123920200-123921600	Active TSS	Brain Substantia Nigra	brain
19	chr12:123920200-123921600	Active TSS	Esophagus	oesophagus
20	chr12:123920200-123921800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr12:123920200-123921800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr12:123920200-123921800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr12:123920200-123921800	Flanking Active TSS	Placenta	Placenta
24	chr12:123920200-123921800	Active TSS	Right Ventricle	heart
25	chr12:123920400-123921400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:123920400-123921400	Active TSS	Primary monocytes fromperipheralblood	blood
27	chr12:123920400-123921400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr12:123920400-123921400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:123920400-123921400	Active TSS	Fetal Brain Female	brain
30	chr12:123920400-123921400	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr12:123920400-123921400	Active TSS	Spleen	Spleen
32	chr12:123920400-123921400	Active TSS	K562	blood
33	chr12:123920400-123921600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:123920400-123921600	Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr12:123920400-123921600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:123920400-123921600	Active TSS	Muscle Satellite Cultured Cells	--
37	chr12:123920400-123921600	Active TSS	Brain Angular Gyrus	brain
38	chr12:123920400-123921600	Active TSS	Brain Anterior Caudate	brain
39	chr12:123920400-123921600	Active TSS	Gastric	stomach
40	chr12:123920400-123921600	Active TSS	Left Ventricle	heart
41	chr12:123920400-123921600	Active TSS	Lung	lung
42	chr12:123920400-123921600	Active TSS	Psoas Muscle	Psoas
43	chr12:123920400-123921600	Active TSS	Rectal Smooth Muscle	rectum
44	chr12:123920400-123921600	Active TSS	Right Atrium	heart
45	chr12:123920400-123921800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
46	chr12:123920400-123921800	Active TSS	H9 Cell Line	embryonic stem cell
47	chr12:123920400-123921800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr12:123920400-123921800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr12:123920400-123921800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr12:123920400-123921800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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