Variant report

Variant	rs12136838
Chromosome Location	chr1:179847355-179847356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:100)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:100 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:179846586-179847443	ECC-1	luminal epithelium:	n/a	n/a
2	RCOR1	chr1:179846841-179847464	K562	blood:	n/a	n/a
3	POLR2A	chr1:179846691-179847374	K562	blood:	n/a	n/a
4	POLR2A	chr1:179846490-179847439	PBDE	blood:	n/a	n/a
5	CTCF	chr1:179846740-179847404	K562	blood:	n/a	chr1:179846975-179846988
6	PML	chr1:179846475-179847441	K562	blood:	n/a	n/a
7	MAX	chr1:179846715-179847398	K562	blood:	n/a	n/a
8	MAX	chr1:179846817-179847399	H1-hESC	embryonic stem cell:	n/a	n/a
9	BHLHE40	chr1:179846836-179847488	K562	blood:	n/a	n/a
10	CREB1	chr1:179846588-179847904	K562	blood:	n/a	n/a
11	POLR2A	chr1:179846572-179847369	H1-neurons	neurons:	n/a	n/a
12	ZMIZ1	chr1:179846633-179847400	K562	blood:	n/a	n/a
13	ARID3A	chr1:179846614-179847471	K562	blood:	n/a	n/a
14	POLR2A	chr1:179846381-179847389	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:179846502-179847385	HUVEC	blood vessel:	n/a	n/a
16	ZNF143	chr1:179846468-179847487	Hela-S3	cervix:	n/a	chr1:179846994-179847012 chr1:179846989-179847008
17	POLR2A	chr1:179846668-179847378	K562	blood:	n/a	n/a
18	TBL1XR1	chr1:179846752-179847425	K562	blood:	n/a	n/a
19	RUNX3	chr1:179846517-179847377	GM12878	blood:	n/a	chr1:179847101-179847110 chr1:179847101-179847110
20	EP300	chr1:179846614-179847434	K562	blood:	n/a	chr1:179846817-179846827
21	CREB1	chr1:179846717-179847380	GM12878	blood:	n/a	n/a
22	MAX	chr1:179846509-179847411	A549	lung:	n/a	n/a
23	POLR2A	chr1:179846662-179847355	GM12878	blood:	n/a	n/a
24	CREB1	chr1:179846665-179847511	K562	blood:	n/a	n/a
25	GTF2F1	chr1:179846823-179847363	H1-hESC	embryonic stem cell:	n/a	n/a
26	HCFC1	chr1:179846483-179847510	K562	blood:	n/a	n/a
27	RCOR1	chr1:179846421-179847511	K562	blood:	n/a	n/a
28	ZNF143	chr1:179846532-179847494	H1-hESC	embryonic stem cell:	n/a	chr1:179846994-179847012 chr1:179846989-179847008
29	MYBL2	chr1:179846669-179847379	HepG2	liver:	n/a	n/a
30	ZC3H11A	chr1:179846645-179847369	K562	blood:	n/a	n/a
31	MTA3	chr1:179846645-179847443	GM12878	blood:	n/a	n/a
32	USF2	chr1:179846815-179847386	GM12878	blood:	n/a	n/a
33	TBL1XR1	chr1:179846677-179847445	K562	blood:	n/a	n/a
34	GABPA	chr1:179846587-179847526	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr1:179846347-179847392	HCT-116	colon:	n/a	n/a
36	POLR2A	chr1:179846667-179847426	Raji	blood:	n/a	n/a
37	CEBPB	chr1:179846887-179847492	K562	blood:	n/a	n/a
38	SIX5	chr1:179846551-179847398	A549	lung:	n/a	n/a
39	GABPA	chr1:179846602-179847483	A549	lung:	n/a	n/a
40	POLR2A	chr1:179845358-179848183	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr1:179846377-179847380	GM12891	blood:	n/a	n/a
42	MAFK	chr1:179846761-179847502	K562	blood:	n/a	n/a
43	REST	chr1:179846485-179847440	A549	lung:	n/a	chr1:179847207-179847225
44	ZNF384	chr1:179846611-179847427	K562	blood:	n/a	n/a
45	POLR2A	chr1:179846470-179847473	H1-hESC	embryonic stem cell:	n/a	n/a
46	IRF1	chr1:179846510-179847459	K562	blood:	n/a	chr1:179846775-179846789
47	CREB1	chr1:179846716-179847535	H1-hESC	embryonic stem cell:	n/a	n/a
48	NR2F2	chr1:179845911-179847504	K562	blood:	n/a	n/a
49	POLR2A	chr1:179846380-179847368	NB4	blood:	n/a	n/a
50	ZKSCAN1	chr1:179846764-179847385	Hela-S3	cervix:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:179847329-179847379	AG04449	skin:	fetal
2	chr1:179847329-179847379	NT2-D1	testis:	n/a
3	chr1:179847329-179847379	NHDF-neo	bronchial:	n/a
4	chr1:179847329-179847379	H1-hESC	embryonic stem cell:	embryo
5	chr1:179847329-179847379	NH-A	brain:	n/a
6	chr1:179847329-179847379	PANC-1	pancreas:	n/a
7	chr1:179847329-179847379	SK-N-MC	brain:	n/a
8	chr1:179847329-179847379	HAEpiC	amniotic membrane:	n/a
9	chr1:179847329-179847379	HCT-116	colon:	n/a
10	chr1:179847329-179847379	MCF-7	breast:	n/a
11	chr1:179847329-179847379	SKMC	muscle:	n/a
12	chr1:179847329-179847379	BE2_C	brain:	n/a
13	chr1:179847329-179847379	A549	lung:	n/a
14	chr1:179847329-179847379	HCF	heart:	n/a
15	chr1:179847329-179847379	BJ	skin:	n/a
16	chr1:179847329-179847379	GM06990	blood:	n/a
17	chr1:179847329-179847379	NB4	blood:	n/a
18	chr1:179847329-179847379	RPTEC	kidney:	n/a
19	chr1:179847329-179847379	SAEC	small airway:	n/a
20	chr1:179847329-179847379	HRCEpiC	kidney:	n/a
21	chr1:179847329-179847379	U87	brain:	n/a
22	chr1:179847329-179847379	AG09319	gingival:	n/a
23	chr1:179847329-179847379	LNCaP	prostate:	n/a
24	chr1:179847329-179847379	CMK	blood:	n/a
25	chr1:179847329-179847379	ProgFib	skin:	n/a
26	chr1:179847329-179847379	HPAEpiC	pulmonary alveolar:	n/a
27	chr1:179847329-179847379	HRPEpiC	eye:	n/a
28	chr1:179847329-179847379	HNPCEpiC	eye:	n/a
29	chr1:179847329-179847379	ovcar-3	ovarian:	n/a
30	chr1:179847329-179847379	SK-N-SH	brain:	n/a
31	chr1:179847329-179847379	SK-N-SH_RA	brain:	n/a
32	chr1:179847329-179847379	HIPEpiC	eye:	n/a
33	chr1:179847329-179847379	IMR90	lung:	fetal
34	chr1:179847329-179847379	HUVEC	blood vessel:	n/a
35	chr1:179847329-179847379	HCM	heart:	n/a
36	chr1:179847329-179847379	Hela-S3	cervix:	n/a
37	chr1:179847329-179847379	HL-60	blood:	n/a
38	chr1:179847329-179847379	ECC-1	luminal epithelium:	n/a
39	chr1:179847329-179847379	HRE	kidney:	n/a
40	chr1:179847329-179847379	MCF10A-Er-Src	breast:	n/a
41	chr1:179847329-179847379	NHBE	bronchial:	n/a
42	chr1:179847329-179847379	Caco-2	colon:	n/a
43	chr1:179847329-179847379	AG04450	lung:	fetal
44	chr1:179847329-179847379	T-47D	breast:	n/a
45	chr1:179847329-179847379	GM12891	blood:	n/a
46	chr1:179847329-179847379	GM19239	blood:	n/a
47	chr1:179847329-179847379	AG10803	skin:	n/a
48	chr1:179847329-179847379	Hepatocyte	liver:	n/a
49	chr1:179847329-179847379	HCPEpiC	choroid plexus:	n/a
50	chr1:179847329-179847379	HepG2	liver:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179843719..179847778-chr1:180121939..180127812,8	K562	blood:
2	chr1:179845348..179847730-chr1:179923811..179926342,3	MCF-7	breast:
3	chr1:179846652..179847400-chr17:70116952..70117487,2	HCT-116	colon:
4	chr1:179832603..179840385-chr1:179843229..179848672,10	MCF-7	breast:
5	chr1:179846797..179847361-chr11:65190227..65191159,2	Hela-S3	cervix:
6	chr1:179845449..179848601-chr1:179867688..179872232,4	K562	blood:
7	chr1:179844894..179847778-chr1:180122782..180124340,2	K562	blood:
8	chr1:179844528..179853403-chr1:179920065..179927793,25	K562	blood:

No data

Variant related genes	Relation type
TOR1AIP2	TF binding region
TOR1AIP1	TF binding region
TOR1AIP1	CpG island
TOR1AIP2	CpG island
ENSG00000258664	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000116260	Chromatin interaction
ENSG00000125398	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000264916	Chromatin interaction
ENSG00000260360	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10913911	1.00[CHB][hapmap]
rs10913912	1.00[CEU][hapmap]
rs10913913	1.00[CHB][hapmap]
rs10913915	1.00[CHB][hapmap]
rs10913926	1.00[CHB][hapmap]
rs11589421	1.00[CHB][hapmap]
rs12117957	1.00[CHB][hapmap]
rs12119285	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124175	1.00[CHB][hapmap]
rs12124336	1.00[CHB][hapmap]
rs12127900	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137562	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12141545	1.00[CHB][hapmap]
rs12144653	1.00[ASN][1000 genomes]
rs61826279	1.00[AFR][1000 genomes]
rs72708653	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72710643	1.00[ASN][1000 genomes]
rs72710651	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv519273	chr1:179831248-179847877	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179844800-179847400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:179844800-179847400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:179845200-179847400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:179845200-179847400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:179845200-179847400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:179845200-179847400	Active TSS	Right Atrium	heart
7	chr1:179845200-179847600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:179845400-179847400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:179845400-179847400	Active TSS	Psoas Muscle	Psoas
10	chr1:179845400-179847600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr1:179845400-179847600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:179845400-179847600	Active TSS	K562	blood
13	chr1:179845600-179847400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:179845600-179847400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr1:179845600-179847400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:179845600-179847600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:179845600-179847600	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:179845800-179847400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr1:179845800-179847400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr1:179845800-179847400	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr1:179845800-179847400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr1:179846000-179847400	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr1:179846000-179847400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr1:179846000-179847400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:179846000-179847400	Active TSS	Fetal Brain Female	brain
26	chr1:179846000-179847400	Active TSS	Fetal Muscle Trunk	muscle
27	chr1:179846000-179847600	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr1:179846000-179847800	Active TSS	GM12878-XiMat	blood
29	chr1:179846200-179847400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:179846200-179847400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:179846200-179847400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:179846200-179847400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:179846200-179847600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:179846200-179847600	Active TSS	Brain Anterior Caudate	brain
35	chr1:179846200-179847600	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr1:179846400-179847400	Active TSS	Brain Germinal Matrix	brain
37	chr1:179846400-179847400	Active TSS	Esophagus	oesophagus
38	chr1:179846600-179847400	Active TSS	Fetal Brain Male	brain
39	chr1:179846600-179847600	Active TSS	Brain Substantia Nigra	brain
40	chr1:179846800-179847400	Enhancers	Small Intestine	intestine
41	chr1:179846800-179847400	Enhancers	Spleen	Spleen
42	chr1:179847000-179847400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:179847000-179847400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:179847000-179847400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:179847000-179847400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr1:179847000-179847400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:179847000-179847400	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr1:179847000-179847400	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr1:179847000-179847400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr1:179847000-179847400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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