Variant report

Variant	rs1168663
Chromosome Location	chr12:122234089-122234090
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:13)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:122231942-122234684	K562	blood:	n/a	n/a
2	HEY1	chr12:122233913-122235684	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:122231256-122234731	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr12:122233854-122234665	K562	blood:	n/a	n/a
5	POLR2A	chr12:122231155-122237092	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:122233989-122234582	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr12:122229522-122241538	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:122233964-122234649	GM12891	blood:	n/a	n/a
9	POLR2A	chr12:122231247-122234639	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:122231231-122242190	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr12:122233924-122234694	GM12878	blood:	n/a	n/a
12	CHD2	chr12:122234069-122234136	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:122233878-122234686	GM12891	blood:	n/a	n/a
14	POLR2A	chr12:122233930-122234385	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr12:122231989-122234676	K562	blood:	n/a	n/a
16	POLR2A	chr12:122230384-122234714	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr12:122233875-122234728	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:122229221-122241674	GM12892	blood:	n/a	n/a
19	POLR2A	chr12:122233950-122234559	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:122230603-122234670	GM12892	blood:	n/a	n/a
21	POLR2A	chr12:122231188-122234637	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr12:122232010-122234571	HepG2	liver:	n/a	n/a
23	POLR2A	chr12:122231207-122242268	MCF-7	breast:	n/a	n/a
24	POLR2A	chr12:122231668-122234717	K562	blood:	n/a	n/a
25	POLR2A	chr12:122233942-122234731	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:122229368-122234595	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:122231040-122242217	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr12:122233911-122234639	GM12891	blood:	n/a	n/a
29	POLR2A	chr12:122233969-122234099	A549	lung:	n/a	n/a
30	POLR2A	chr12:122233920-122234652	HepG2	liver:	n/a	n/a
31	POLR2A	chr12:122231410-122236435	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr12:122231900-122238487	K562	blood:	n/a	n/a
33	POLR2A	chr12:122231709-122243601	K562	blood:	n/a	n/a
34	POLR2A	chr12:122233904-122234668	HL-60	blood:	n/a	n/a
35	MYBL2	chr12:122234013-122234600	HepG2	liver:	n/a	n/a
36	POLR2A	chr12:122233899-122234398	HCT-116	colon:	n/a	n/a
37	POLR2A	chr12:122229262-122234581	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr12:122233931-122234722	HepG2	liver:	n/a	n/a
39	POLR2A	chr12:122229711-122234710	H1-neurons	neurons:	n/a	n/a
40	POLR2A	chr12:122229178-122242172	GM12878	blood:	n/a	n/a
41	POLR2A	chr12:122229777-122242191	HepG2	liver:	n/a	n/a
42	HEY1	chr12:122233937-122234667	HepG2	liver:	n/a	n/a
43	POLR2A	chr12:122233862-122234122	A549	lung:	n/a	n/a
44	POLR2A	chr12:122233850-122234109	H1-hESC	embryonic stem cell:	n/a	n/a
45	MYBL2	chr12:122234041-122234643	HepG2	liver:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122233308..122235203-chr20:46415210..46416996,2	MCF-7	breast:
2	chr12:122145450..122152863-chr12:122233897..122241914,16	MCF-7	breast:
3	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
4	chr12:122233178..122236048-chr16:88921009..88923883,2	MCF-7	breast:
5	chr12:121974972..121977558-chr12:122231894..122235040,4	MCF-7	breast:
6	chr12:121836495..121838050-chr12:122231938..122234187,2	K562	blood:
7	chr12:122231564..122242843-chr12:122324518..122333366,33	K562	blood:
8	chr12:122232180..122234901-chr12:122344222..122346588,2	K562	blood:
9	chr12:122233682..122234604-chr17:7387298..7388221,2	HCT-116	colon:
10	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
11	chr12:122233788..122236172-chr12:122398855..122400644,2	MCF-7	breast:
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:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RHOF-1	chr12:122233173-122234148	ENSG00000212694.4
2	lnc-RHOF-1	chr12:122233896-122234148	ENSG00000212694.4
3	lnc-RHOF-1	chr12:122233546-122234148	ENSG00000212694.4
4	lnc-RHOF-1	chr12:122233183-122234785	ENSG00000212694.4
5	lnc-RHOF-1	chr12:122233799-122234148	ENSG00000212694.4
6	lnc-SETD1B-3	chr12:122233120-122234144	NONHSAT031445
7	lnc-RHOF-1	chr12:122233182-122234928	NONHSAT031452
8	lnc-RHOF-1	chr12:122233219-122234148	NONHSAT031458
9	lnc-RHOF-1	chr12:122233637-122234150	NONHSAT031461
10	lnc-RHOF-1	chr12:122233178-122236657	NONHSAT031451
11	lnc-RHOF-1	chr12:122233165-122234148	NONHSAT031446
12	lnc-RHOF-1	chr12:122233201-122234148	NONHSAT031456
13	lnc-RHOF-1	chr12:122233204-122234148	NONHSAT031457

No data

Variant related genes	Relation type
ENSG00000272849	TF binding region
RHOF	TF binding region
ENSG00000188735	Chromatin interaction
ENSG00000256742	Chromatin interaction
ENSG00000239082	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000167515	Chromatin interaction
ENSG00000141012	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000089053	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000170633	Chromatin interaction
ENSG00000175727	Chromatin interaction
ENSG00000256950	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1004390	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11043202	0.88[EUR][1000 genomes]
rs11043203	0.88[EUR][1000 genomes]
rs1168664	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168665	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168666	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168668	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168669	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168671	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168672	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168673	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11837955	0.81[ASN][1000 genomes]
rs12303659	0.81[ASN][1000 genomes]
rs12307227	0.87[EUR][1000 genomes]
rs12832268	0.86[ASN][1000 genomes]
rs12832320	0.86[ASN][1000 genomes]
rs1667578	0.88[EUR][1000 genomes]
rs1667579	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1795965	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1795966	0.81[AMR][1000 genomes]
rs2019561	0.89[EUR][1000 genomes]
rs2019562	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2122266	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2707066	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2707067	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28493021	0.86[ASN][1000 genomes]
rs34226605	0.86[ASN][1000 genomes]
rs712852	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136373	0.86[ASN][1000 genomes]
rs7300684	0.86[ASN][1000 genomes]
rs7308123	0.86[ASN][1000 genomes]
rs7308348	0.86[ASN][1000 genomes]
rs73413732	0.83[ASN][1000 genomes]
rs7957564	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7974348	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs895951	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs895952	0.88[EUR][1000 genomes]
rs895953	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs895954	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs895957	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs921286	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs921287	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs930665	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1168663	AC084018.1	cis	Skin Sun Exposed Lower leg	GTEx
rs1168663	AC084018.1	cis	Artery Tibial	GTEx
rs1168663	LOC338799	cis	occipital cortex	BrainEAC
rs1168663	LOC338799	cis	brain	BrainEAC

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	chr12:122231400-122235000	Flanking Active TSS	HepG2	liver
4	chr12:122232200-122234200	Weak transcription	Ovary	ovary
5	chr12:122232200-122234200	Enhancers	HSMMtube	muscle
6	chr12:122232200-122235000	Enhancers	Left Ventricle	heart
7	chr12:122232200-122235400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:122232200-122236600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:122232400-122236600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:122232600-122234200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:122232800-122234400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:122232800-122234600	Genic enhancers	Brain Anterior Caudate	brain
13	chr12:122232800-122234600	Enhancers	Small Intestine	intestine
14	chr12:122232800-122234800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:122232800-122235400	Weak transcription	Aorta	Aorta
16	chr12:122232800-122238000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:122233000-122234200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:122233000-122234200	Genic enhancers	Brain Inferior Temporal Lobe	brain
19	chr12:122233000-122234200	Genic enhancers	Esophagus	oesophagus
20	chr12:122233000-122234200	Genic enhancers	Rectal Smooth Muscle	rectum
21	chr12:122233000-122234400	Enhancers	Brain Cingulate Gyrus	brain
22	chr12:122233000-122234400	Genic enhancers	Right Ventricle	heart
23	chr12:122233000-122234400	Genic enhancers	A549	lung
24	chr12:122233000-122234400	Enhancers	HSMM	muscle
25	chr12:122233000-122234400	Genic enhancers	K562	blood
26	chr12:122233000-122234600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:122233000-122234600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:122233000-122234600	Genic enhancers	Brain Substantia Nigra	brain
29	chr12:122233000-122234600	Genic enhancers	Gastric	stomach
30	chr12:122233000-122234600	Genic enhancers	Stomach Mucosa	stomach
31	chr12:122233000-122234800	Genic enhancers	Adipose Nuclei	Adipose
32	chr12:122233000-122234800	Genic enhancers	Brain Hippocampus Middle	brain
33	chr12:122233000-122234800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:122233000-122234800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr12:122233000-122234800	Genic enhancers	Fetal Muscle Leg	muscle
36	chr12:122233000-122234800	Genic enhancers	NHLF	lung
37	chr12:122233000-122235000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:122233000-122235000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:122233000-122235000	Genic enhancers	Fetal Intestine Large	intestine
40	chr12:122233000-122235000	Genic enhancers	Fetal Intestine Small	intestine
41	chr12:122233000-122235000	Enhancers	Pancreas	Pancrea
42	chr12:122233000-122235000	Enhancers	HMEC	breast
43	chr12:122233000-122235200	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr12:122233000-122235800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr12:122233000-122235800	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
46	chr12:122233000-122236000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:122233000-122236000	Genic enhancers	Fetal Stomach	stomach
48	chr12:122233000-122236000	Genic enhancers	Fetal Thymus	thymus
49	chr12:122233000-122236800	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr12:122233000-122237000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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