Variant report

Variant	rs712852
Chromosome Location	chr12:122233495-122233496
allele	C/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	chr12:122232008-122233687	K562	blood:	n/a	n/a
2	POLR2A	chr12:122231913-122233948	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:122231942-122234684	K562	blood:	n/a	n/a
4	POLR2A	chr12:122231256-122234731	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr12:122231155-122237092	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:122231262-122233824	GM12891	blood:	n/a	n/a
7	POLR2A	chr12:122231991-122233867	GM12891	blood:	n/a	n/a
8	POLR2A	chr12:122231286-122233689	A549	lung:	n/a	n/a
9	POLR2A	chr12:122231910-122233704	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:122231318-122233921	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:122229522-122241538	HepG2	liver:	n/a	n/a
12	BCL3	chr12:122229500-122233523	A549	lung:	n/a	chr12:122231001-122231010 chr12:122229915-122229923 chr12:122231561-122231570 chr12:122231384-122231397 chr12:122232267-122232280 chr12:122231383-122231396
13	POLR2A	chr12:122230693-122233942	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:122232014-122233778	GM12892	blood:	n/a	n/a
15	POLR2A	chr12:122231642-122233853	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr12:122231272-122233893	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:122231968-122233602	HUVEC	blood vessel:	n/a	n/a
18	ZEB1	chr12:122229267-122233709	HepG2	liver:	n/a	n/a
19	POLR2A	chr12:122231247-122234639	GM12878	blood:	n/a	n/a
20	CTCF	chr12:122231441-122233504	HCT-116	colon:	n/a	chr12:122233004-122233014 chr12:122232237-122232255 chr12:122232310-122232328 chr12:122232999-122233017 chr12:122232322-122232335 chr12:122233001-122233022 chr12:122232312-122232325 chr12:122233002-122233015 chr12:122233000-122233016 chr12:122232299-122232308 chr12:122233002-122233011
21	POLR2A	chr12:122231231-122242190	PANC-1	pancreas:	n/a	n/a
22	SMARCB1	chr12:122229367-122233602	Hela-S3	cervix:	n/a	chr12:122230186-122230195
23	CREB1	chr12:122229519-122233581	HepG2	liver:	n/a	n/a
24	POLR2A	chr12:122230689-122233658	GM18951	blood:	n/a	n/a
25	POLR2A	chr12:122231941-122233695	PBDE	blood:	n/a	n/a
26	POLR2A	chr12:122231989-122234676	K562	blood:	n/a	n/a
27	POLR2A	chr12:122230384-122234714	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr12:122229543-122233541	GM12892	blood:	n/a	n/a
29	MAX	chr12:122229426-122233619	A549	lung:	n/a	chr12:122231986-122231996 chr12:122231622-122231632
30	POLR2A	chr12:122229221-122241674	GM12892	blood:	n/a	n/a
31	POLR2A	chr12:122233444-122233607	A549	lung:	n/a	n/a
32	POLR2A	chr12:122231876-122233800	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:122231430-122233865	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr12:122233414-122233505	MCF-7	breast:	n/a	n/a
35	POLR2A	chr12:122230603-122234670	GM12892	blood:	n/a	n/a
36	POLR2A	chr12:122233246-122233619	HepG2	liver:	n/a	n/a
37	JUN	chr12:122231479-122233625	K562	blood:	n/a	chr12:122231914-122231923 chr12:122231602-122231611 chr12:122232326-122232337
38	PML	chr12:122229506-122233753	GM12878	blood:	n/a	n/a
39	POLR2A	chr12:122231245-122233786	PFSK-1	brain:	n/a	n/a
40	MXI1	chr12:122231296-122233681	IMR90	lung:	n/a	n/a
41	POLR2A	chr12:122231188-122234637	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr12:122232010-122234571	HepG2	liver:	n/a	n/a
43	TCF12	chr12:122229223-122233557	A549	lung:	n/a	chr12:122233009-122233019 chr12:122231871-122231881 chr12:122232576-122232586
44	REST	chr12:122231390-122233530	H1-neurons	neurons:	n/a	chr12:122231995-122232015 chr12:122233012-122233025 chr12:122231996-122232014
45	MBD4	chr12:122231914-122233591	HepG2	liver:	n/a	n/a
46	POLR2A	chr12:122231207-122242268	MCF-7	breast:	n/a	n/a
47	POLR2A	chr12:122229401-122233785	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr12:122232053-122233855	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr12:122231668-122234717	K562	blood:	n/a	n/a
50	POLR2A	chr12:122229368-122234595	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122233308..122235203-chr20:46415210..46416996,2	MCF-7	breast:
2	chr12:122230934..122233822-chr12:122459500..122463009,3	MCF-7	breast:
3	chr12:122232032..122233517-chr12:122325701..122326925,10	MCF-7	breast:
4	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
5	chr12:122233178..122236048-chr16:88921009..88923883,2	MCF-7	breast:
6	chr12:121974972..121977558-chr12:122231894..122235040,4	MCF-7	breast:
7	chr12:121836495..121838050-chr12:122231938..122234187,2	K562	blood:
8	chr12:122231564..122242843-chr12:122324518..122333366,33	K562	blood:
9	chr1:116445666..116447671-chr12:122232460..122234006,2	MCF-7	breast:
10	chr12:122232180..122234901-chr12:122344222..122346588,2	K562	blood:
11	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
12	chr12:122017334..122020292-chr12:122231782..122234542,4	K562	blood:
13	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:
14	chr12:122232866..122235205-chr12:122514967..122518209,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RHOF-1	chr12:122233173-122234148	ENSG00000212694.4
2	lnc-RHOF-1	chr12:122233173-122233632	ENSG00000212694.4
3	lnc-RHOF-1	chr12:122233183-122234785	ENSG00000212694.4
4	lnc-SETD1B-3	chr12:122233120-122234144	NONHSAT031445
5	lnc-RHOF-1	chr12:122233178-122233632	NONHSAT031449
6	lnc-RHOF-1	chr12:122233178-122233632	NONHSAT031450
7	lnc-RHOF-1	chr12:122233182-122234928	NONHSAT031452
8	lnc-RHOF-1	chr12:122233187-122233632	NONHSAT031454
9	lnc-RHOF-1	chr12:122233194-122233632	NONHSAT031455
10	lnc-RHOF-1	chr12:122233219-122234148	NONHSAT031458
11	lnc-RHOF-1	chr12:122233178-122236657	NONHSAT031451
12	lnc-RHOF-1	chr12:122233165-122234148	NONHSAT031446
13	lnc-RHOF-1	chr12:122233476-122233632	ENSG00000212694.4
14	lnc-RHOF-1	chr12:122233201-122234148	NONHSAT031456
15	lnc-RHOF-1	chr12:122233204-122234148	NONHSAT031457

Variant related genes	Relation type
ENSG00000272849	TF binding region
RHOF	TF binding region
ENSG00000196562	Chromatin interaction
ENSG00000167515	Chromatin interaction
ENSG00000170633	Chromatin interaction
ENSG00000256742	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000089053	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000175727	Chromatin interaction
ENSG00000141012	Chromatin interaction
ENSG00000239082	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1004390	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11043202	0.89[EUR][1000 genomes]
rs11043203	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11043207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs1168663	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168664	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168665	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1168666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168668	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168669	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1168671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168672	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1168673	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837955	0.81[ASN][1000 genomes]
rs12303659	0.81[ASN][1000 genomes]
rs12307227	0.88[EUR][1000 genomes]
rs12832268	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12832320	0.86[ASN][1000 genomes]
rs1667578	0.89[EUR][1000 genomes]
rs1667579	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795965	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1795966	0.83[AMR][1000 genomes]
rs2019561	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2019562	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2122266	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2707066	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2707067	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28493021	0.86[ASN][1000 genomes]
rs34226605	0.86[ASN][1000 genomes]
rs7136373	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7300684	0.86[ASN][1000 genomes]
rs7308123	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7308348	0.86[ASN][1000 genomes]
rs73413732	0.83[ASN][1000 genomes]
rs7957564	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895951	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs895952	0.89[EUR][1000 genomes]
rs895953	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs895954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895957	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs921286	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs921287	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs930665	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs712852	AC084018.1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122229600-122235400	Enhancers	Fetal Heart	heart
2	chr12:122230800-122236400	Enhancers	Fetal Brain Male	brain
3	chr12:122231400-122233600	Flanking Active TSS	Liver	Liver
4	chr12:122231400-122233800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr12:122231400-122235000	Flanking Active TSS	HepG2	liver
6	chr12:122232200-122233600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:122232200-122233600	Enhancers	Placenta Amnion	Placenta Amnion
8	chr12:122232200-122234200	Weak transcription	Ovary	ovary
9	chr12:122232200-122234200	Enhancers	HSMMtube	muscle
10	chr12:122232200-122235000	Enhancers	Left Ventricle	heart
11	chr12:122232200-122235400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:122232200-122236600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:122232400-122236600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:122232600-122233600	Enhancers	HUVEC	blood vessel
15	chr12:122232600-122234200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:122232800-122234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:122232800-122234400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:122232800-122234600	Genic enhancers	Brain Anterior Caudate	brain
19	chr12:122232800-122234600	Enhancers	Small Intestine	intestine
20	chr12:122232800-122234800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:122232800-122235400	Weak transcription	Aorta	Aorta
22	chr12:122232800-122238000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:122233000-122233600	Enhancers	H1 Cell Line	embryonic stem cell
24	chr12:122233000-122233600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:122233000-122233600	Enhancers	Primary hematopoietic stem cells	blood
26	chr12:122233000-122233600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr12:122233000-122233600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr12:122233000-122234000	Genic enhancers	Colon Smooth Muscle	Colon
29	chr12:122233000-122234200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:122233000-122234200	Genic enhancers	Brain Inferior Temporal Lobe	brain
31	chr12:122233000-122234200	Genic enhancers	Esophagus	oesophagus
32	chr12:122233000-122234200	Genic enhancers	Rectal Smooth Muscle	rectum
33	chr12:122233000-122234400	Enhancers	Brain Cingulate Gyrus	brain
34	chr12:122233000-122234400	Genic enhancers	Right Ventricle	heart
35	chr12:122233000-122234400	Genic enhancers	A549	lung
36	chr12:122233000-122234400	Enhancers	HSMM	muscle
37	chr12:122233000-122234400	Genic enhancers	K562	blood
38	chr12:122233000-122234600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr12:122233000-122234600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:122233000-122234600	Genic enhancers	Brain Substantia Nigra	brain
41	chr12:122233000-122234600	Genic enhancers	Gastric	stomach
42	chr12:122233000-122234600	Genic enhancers	Stomach Mucosa	stomach
43	chr12:122233000-122234800	Genic enhancers	Adipose Nuclei	Adipose
44	chr12:122233000-122234800	Genic enhancers	Brain Hippocampus Middle	brain
45	chr12:122233000-122234800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:122233000-122234800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr12:122233000-122234800	Genic enhancers	Fetal Muscle Leg	muscle
48	chr12:122233000-122234800	Genic enhancers	NHLF	lung
49	chr12:122233000-122235000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:122233000-122235000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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