Variant report

Variant	rs12004004
Chromosome Location	chr9:95056231-95056232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:661)
CpG islands
(count:61)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:661 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:95054862-95057471	MCF10A-Er-Src	breast:	n/a	n/a
2	TAL1	chr9:95055513-95057180	K562	blood:	n/a	n/a
3	USF2	chr9:95055869-95056530	Hela-S3	cervix:	n/a	n/a
4	USF1	chr9:95055858-95056339	ECC-1	luminal epithelium:	n/a	n/a
5	SIN3AK20	chr9:95055720-95056358	H1-hESC	embryonic stem cell:	n/a	n/a
6	FOS	chr9:95055855-95056350	Hela-S3	cervix:	n/a	n/a
7	CHD2	chr9:95055795-95056407	HepG2	liver:	n/a	n/a
8	TAF1	chr9:95055787-95056350	HepG2	liver:	n/a	n/a
9	CTCF	chr9:95056160-95056310	NB4	blood:	n/a	n/a
10	POLR2A	chr9:95055732-95056412	HepG2	liver:	n/a	n/a
11	REST	chr9:95055803-95056341	SK-N-SH	brain:	n/a	chr9:95056180-95056193 chr9:95056192-95056205 chr9:95056192-95056205 chr9:95056189-95056202
12	POLR2A	chr9:95055524-95057064	Hela-S3	cervix:	n/a	n/a
13	UBTF	chr9:95055729-95057092	K562	blood:	n/a	n/a
14	EGR1	chr9:95055925-95056261	K562	blood:	n/a	n/a
15	TAF7	chr9:95055652-95056500	H1-hESC	embryonic stem cell:	n/a	n/a
16	JUND	chr9:95055730-95056455	H1-hESC	embryonic stem cell:	n/a	n/a
17	PAX5	chr9:95055714-95056437	GM12878	blood:	n/a	n/a
18	CTCF	chr9:95056100-95056250	HPAF	blood vessel:	n/a	chr9:95056153-95056166
19	ELK1	chr9:95055781-95056458	GM12878	blood:	n/a	n/a
20	JUND	chr9:95055789-95056300	HepG2	liver:	n/a	n/a
21	SIN3AK20	chr9:95055769-95056289	PFSK-1	brain:	n/a	n/a
22	MYC	chr9:95055821-95056397	GM12878	blood:	n/a	n/a
23	CTCF	chr9:95056100-95056250	HMF	breast:	n/a	chr9:95056153-95056166
24	POLR2A	chr9:95055774-95056367	HepG2	liver:	n/a	n/a
25	POLR2A	chr9:95055697-95056437	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr9:95056100-95056250	Hela-S3	cervix:	n/a	chr9:95056153-95056166
27	POLR2A	chr9:95055619-95056478	HCT-116	colon:	n/a	n/a
28	RFX5	chr9:95055812-95056341	GM12878	blood:	n/a	chr9:95056038-95056047
29	HA-E2F1	chr9:95055685-95056445	MCF-7	breast:	n/a	chr9:95056084-95056093 chr9:95056037-95056046
30	CTCF	chr9:95056120-95056270	GM12872	blood:	n/a	chr9:95056153-95056166
31	CTCF	chr9:95056022-95056256	SK-N-SH_RA	brain:	n/a	chr9:95056153-95056166
32	GTF2F1	chr9:95055743-95056358	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr9:95056120-95056270	A549	lung:	n/a	chr9:95056153-95056166
34	MYC	chr9:95055815-95056362	MCF-7	breast:	n/a	n/a
35	IRF1	chr9:95054819-95056439	K562	blood:	n/a	chr9:95055876-95055885 chr9:95056037-95056046 chr9:95055390-95055401
36	CHD1	chr9:95055777-95056473	GM12878	blood:	n/a	n/a
37	CEBPB	chr9:95055577-95056491	HCT-116	colon:	n/a	n/a
38	CTCF	chr9:95056160-95056310	WI-38	lung:	n/a	n/a
39	POLR2A	chr9:95048736-95059563	K562	blood:	n/a	n/a
40	ZBTB7A	chr9:95056101-95056350	K562	blood:	n/a	chr9:95056283-95056290
41	CTCF	chr9:95056118-95056265	GM13977	blood:	n/a	chr9:95056153-95056166
42	POLR2A	chr9:95055618-95057079	GM12892	blood:	n/a	n/a
43	EP300	chr9:95055921-95056449	K562	blood:	n/a	chr9:95056319-95056329 chr9:95056385-95056392
44	CTCF	chr9:95056021-95056348	A549	lung:	n/a	chr9:95056153-95056166
45	HEY1	chr9:95055715-95056442	HepG2	liver:	n/a	n/a
46	ZKSCAN1	chr9:95055797-95056364	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr9:95055944-95056341	T-47D	breast:	n/a	chr9:95056153-95056166
48	YY1	chr9:95055793-95056275	GM12892	blood:	n/a	n/a
49	BCL3	chr9:95055680-95056499	A549	lung:	n/a	n/a
50	CTCF	chr9:95056180-95056330	NHDF-neo	bronchial:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:95056231-95056281	PFSK-1	brain:	n/a
2	chr9:95056231-95056281	T-47D	breast:	n/a
3	chr9:95056231-95056281	HNPCEpiC	eye:	n/a
4	chr9:95056231-95056281	AG04450	lung:	fetal
5	chr9:95056231-95056281	Caco-2	colon:	n/a
6	chr9:95056231-95056281	AG10803	skin:	n/a
7	chr9:95056231-95056281	LNCaP	prostate:	n/a
8	chr9:95056231-95056281	SK-N-SH	brain:	n/a
9	chr9:95056231-95056281	AoSMC	blood vessel:	n/a
10	chr9:95056231-95056281	RPTEC	kidney:	n/a
11	chr9:95056231-95056281	PANC-1	pancreas:	n/a
12	chr9:95056231-95056281	PrEC	prostate:	n/a
13	chr9:95056231-95056281	ovcar-3	ovarian:	n/a
14	chr9:95056231-95056281	Jurkat	blood:	n/a
15	chr9:95056231-95056281	AG09319	gingival:	n/a
16	chr9:95056231-95056281	MCF-7	breast:	n/a
17	chr9:95056231-95056281	BJ	skin:	n/a
18	chr9:95056231-95056281	GM06990	blood:	n/a
19	chr9:95056231-95056281	NB4	blood:	n/a
20	chr9:95056231-95056281	MCF10A-Er-Src	breast:	n/a
21	chr9:95056231-95056281	HEK293	kidney:	embryo
22	chr9:95056231-95056281	Hepatocyte	liver:	n/a
23	chr9:95056231-95056281	HL-60	blood:	n/a
24	chr9:95056231-95056281	SK-N-SH_RA	brain:	n/a
25	chr9:95056231-95056281	A549	lung:	n/a
26	chr9:95056231-95056281	SK-N-MC	brain:	n/a
27	chr9:95056231-95056281	CMK	blood:	n/a
28	chr9:95056231-95056281	HCM	heart:	n/a
29	chr9:95056231-95056281	SKMC	muscle:	n/a
30	chr9:95056231-95056281	NHBE	bronchial:	n/a
31	chr9:95056231-95056281	IMR90	lung:	fetal
32	chr9:95056231-95056281	ECC-1	luminal epithelium:	n/a
33	chr9:95056231-95056281	HUVEC	blood vessel:	n/a
34	chr9:95056231-95056281	K562	blood:	n/a
35	chr9:95056231-95056281	NH-A	brain:	n/a
36	chr9:95056231-95056281	HMEC	breast:	n/a
37	chr9:95056231-95056281	HEEpiC	esophagus:	n/a
38	chr9:95056231-95056281	HRE	kidney:	n/a
39	chr9:95056231-95056281	U87	brain:	n/a
40	chr9:95056231-95056281	H1-hESC	embryonic stem cell:	embryo
41	chr9:95056231-95056281	BE2_C	brain:	n/a
42	chr9:95056231-95056281	NHDF-neo	bronchial:	n/a
43	chr9:95056231-95056281	AG04449	skin:	fetal
44	chr9:95056231-95056281	GM12878	blood:	n/a
45	chr9:95056231-95056281	GM12891	blood:	n/a
46	chr9:95056231-95056281	HCF	heart:	n/a
47	chr9:95056231-95056281	HRPEpiC	eye:	n/a
48	chr9:95056231-95056281	HRCEpiC	kidney:	n/a
49	chr9:95056231-95056281	AG09309	skin:	n/a
50	chr9:95056231-95056281	GM12892	blood:	n/a

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95052267..95059743-chr9:95085805..95090654,23	MCF-7	breast:
2	chr12:104680398..104681014-chr9:95055895..95056419,2	NB4	blood:
3	chr9:94996019..94998973-chr9:95056165..95057730,2	MCF-7	breast:
4	chr9:94876692..94878485-chr9:95054878..95056695,2	MCF-7	breast:
5	chr9:94899081..94901349-chr9:95056061..95058658,2	K562	blood:
6	chr9:95054612..95057091-chr9:95526187..95528018,2	K562	blood:
7	chr9:95000607..95005891-chr9:95055882..95059515,6	K562	blood:
8	chr9:95056040..95058266-chr9:95225229..95227656,2	K562	blood:
9	chr19:49990556..49991246-chr9:95055908..95056438,2	Hela-S3	cervix:
10	chr20:55926188..55927994-chr9:95055648..95058175,2	MCF-7	breast:
11	chr9:94897363..94901349-chr9:95056061..95059787,4	K562	blood:
12	chr9:95051112..95065542-chr9:95079443..95091389,38	K562	blood:
13	chr9:95004787..95006514-chr9:95054473..95056425,2	K562	blood:
14	chr9:95052930..95062724-chr9:95083607..95090664,16	MCF-7	breast:
15	chr13:115000124..115000635-chr9:95056223..95056723,2	NB4	blood:
16	chr9:95041855..95050591-chr9:95053528..95058799,10	MCF-7	breast:
17	chr9:94923018..94924668-chr9:95056057..95058529,2	K562	blood:
18	chr9:94907173..94909059-chr9:95054876..95056486,2	MCF-7	breast:
19	chr9:95056178..95058167-chr9:95374802..95377179,2	K562	blood:
20	chr16:71495701..71496536-chr9:95055685..95056447,2	HCT-116	colon:
21	chr9:94875730..94878651-chr9:95055011..95057658,2	K562	blood:

No data

Variant related genes	Relation type
IARS	TF binding region
SNORA84	TF binding region
IARS	CpG island
SNORA84	CpG island
ENSG00000196305	Chromatin interaction
ENSG00000167377	Chromatin interaction
ENSG00000198000	Chromatin interaction
ENSG00000238996	Chromatin interaction
ENSG00000130177	Chromatin interaction
ENSG00000101146	Chromatin interaction
ENSG00000142541	Chromatin interaction
ENSG00000247324	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000185963	Chromatin interaction
ENSG00000188312	Chromatin interaction
ENSG00000090054	Chromatin interaction
ENSG00000225511	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12001812	1.00[AMR][1000 genomes]
rs12002188	1.00[AMR][1000 genomes]
rs34355623	1.00[AMR][1000 genomes]
rs7046734	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 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	chr9:95053400-95056600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:95053600-95057200	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr9:95054000-95056800	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr9:95054200-95057200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr9:95054400-95057200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr9:95054400-95057200	Active TSS	A549	lung
7	chr9:95054600-95057000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr9:95054600-95057000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:95054600-95057400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr9:95054800-95056600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr9:95054800-95056600	Active TSS	Muscle Satellite Cultured Cells	--
12	chr9:95055000-95056400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:95055000-95056400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:95055000-95056600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:95055000-95056600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:95055000-95056600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:95055000-95056600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr9:95055000-95056600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:95055000-95056600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:95055000-95056600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:95055000-95056600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:95055000-95056600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:95055000-95056600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:95055000-95056600	Active TSS	Fetal Intestine Small	intestine
25	chr9:95055000-95056600	Active TSS	Fetal Muscle Leg	muscle
26	chr9:95055000-95056600	Active TSS	Right Ventricle	heart
27	chr9:95055000-95056600	Active TSS	Stomach Mucosa	stomach
28	chr9:95055000-95056600	Active TSS	HSMM	muscle
29	chr9:95055000-95056600	Active TSS	K562	blood
30	chr9:95055000-95056600	Active TSS	NHDF-Ad	bronchial
31	chr9:95055000-95056800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:95055000-95056800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:95055000-95056800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:95055000-95056800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:95055000-95056800	Active TSS	Psoas Muscle	Psoas
36	chr9:95055000-95056800	Active TSS	HSMMtube	muscle
37	chr9:95055000-95057000	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr9:95055000-95057000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr9:95055000-95057000	Active TSS	Right Atrium	heart
40	chr9:95055000-95057000	Active TSS	GM12878-XiMat	blood
41	chr9:95055000-95057200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr9:95055000-95057200	Active TSS	H1 Cell Line	embryonic stem cell
43	chr9:95055200-95056400	Active TSS	Primary T cells fromperipheralblood	blood
44	chr9:95055200-95056400	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr9:95055200-95056400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:95055200-95056400	Bivalent/Poised TSS	HepG2	liver
47	chr9:95055200-95056600	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr9:95055200-95056600	Active TSS	Colonic Mucosa	Colon
49	chr9:95055200-95056600	Active TSS	Fetal Brain Male	brain
50	chr9:95055200-95056600	Active TSS	Fetal Brain Female	brain

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