Variant report

Variant	rs3138143
Chromosome Location	chr12:56115030-56115031
allele	C/T
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	CHD2	chr12:56114859-56115106	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr12:56114900-56115050	GM12864	blood:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
3	MAX	chr12:56114743-56115365	MCF-7	breast:	n/a	n/a
4	USF1	chr12:56114755-56115183	A549	lung:	n/a	n/a
5	PBX3	chr12:56114571-56115880	SK-N-SH	brain:	n/a	n/a
6	RAD21	chr12:56114686-56115262	MCF-7	breast:	n/a	chr12:56114934-56114953
7	CTCF	chr12:56114632-56115640	SK-N-SH	brain:	n/a	chr12:56114707-56114715 chr12:56114931-56114952 chr12:56114936-56114954
8	RXRA	chr12:56114712-56115035	HepG2	liver:	n/a	chr12:56114879-56114893
9	CTCF	chr12:56114900-56115050	AG04449	skin:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
10	CREB1	chr12:56114852-56115163	A549	lung:	n/a	n/a
11	CTCF	chr12:56114679-56115206	A549	lung:	n/a	chr12:56114707-56114715 chr12:56114931-56114952 chr12:56114936-56114954
12	RAD21	chr12:56114601-56115168	SK-N-SH_RA	brain:	n/a	chr12:56114934-56114953
13	POLR2A	chr12:56114860-56116296	HUVEC	blood vessel:	n/a	n/a
14	CTCF	chr12:56114835-56115091	MCF-7	breast:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
15	CTCF	chr12:56114823-56115082	Pancreas_OC	pancreas:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
16	FOXA1	chr12:56114770-56115105	T-47D	breast:	n/a	n/a
17	TCF12	chr12:56114748-56115508	ECC-1	luminal epithelium:	n/a	n/a
18	MYBL2	chr12:56114597-56115096	HepG2	liver:	n/a	n/a
19	CTCF	chr12:56114845-56115045	SK-N-SH_RA	brain:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
20	RAD21	chr12:56114704-56115109	A549	lung:	n/a	chr12:56114934-56114953
21	EP300	chr12:56114460-56115488	SK-N-SH	brain:	n/a	n/a
22	FOS	chr12:56114757-56115210	MCF10A-Er-Src	breast:	n/a	chr12:56115073-56115084
23	POLR2A	chr12:56113532-56124497	U87	brain:	n/a	n/a
24	RAD21	chr12:56114577-56115309	ECC-1	luminal epithelium:	n/a	chr12:56114934-56114953
25	RAD21	chr12:56114757-56115116	HepG2	liver:	n/a	chr12:56114934-56114953
26	CTCF	chr12:56114880-56115030	SAEC	small airway:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
27	CTCF	chr12:56114844-56115072	GM19240	blood:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
28	POLR2A	chr12:56114962-56115370	MCF-7	breast:	n/a	n/a
29	CTCF	chr12:56114802-56115091	Hela-S3	cervix:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
30	CTCF	chr12:56114920-56115070	GM12865	blood:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
31	CTCF	chr12:56114834-56115111	MCF-7	breast:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
32	STAT5A	chr12:56114594-56115111	GM12878	blood:	n/a	n/a
33	ZKSCAN1	chr12:56114858-56115145	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr12:56114900-56115050	AG09309	skin:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
35	EP300	chr12:56114613-56115272	SK-N-SH_RA	brain:	n/a	n/a
36	RAD21	chr12:56114821-56115033	K562	blood:	n/a	chr12:56114934-56114953
37	NFIC	chr12:56114493-56115507	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr12:56114691-56115837	ECC-1	luminal epithelium:	n/a	n/a
39	CTCF	chr12:56114920-56115070	HL-60	blood:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
40	POLR2A	chr12:56114779-56115305	HCT-116	colon:	n/a	n/a
41	CTCF	chr12:56114900-56115050	GM12872	blood:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
42	CTCF	chr12:56114920-56115070	AG04450	lung:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
43	GTF2F1	chr12:56114799-56115058	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr12:56114837-56115062	GM10266	blood:	n/a	chr12:56114931-56114952 chr12:56114936-56114954
45	STAT3	chr12:56114766-56115085	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr12:56114616-56115992	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr12:56114597-56115220	SK-N-SH	brain:	n/a	n/a
48	RAD21	chr12:56114761-56115140	HepG2	liver:	n/a	chr12:56114934-56114953
49	MYC	chr12:56114821-56115135	HUVEC	blood vessel:	n/a	n/a
50	ELK1	chr12:56114926-56115078	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:56115029-56115079	HIPEpiC	eye:	n/a
2	chr12:56115029-56115079	PANC-1	pancreas:	n/a
3	chr12:56115029-56115079	HPAEpiC	pulmonary alveolar:	n/a
4	chr12:56115029-56115079	LNCaP	prostate:	n/a
5	chr12:56115029-56115079	NHDF-neo	bronchial:	n/a
6	chr12:56115029-56115079	MCF10A-Er-Src	breast:	n/a
7	chr12:56115029-56115079	GM06990	blood:	n/a
8	chr12:56115029-56115079	SK-N-SH_RA	brain:	n/a
9	chr12:56115029-56115079	GM19239	blood:	n/a
10	chr12:56115029-56115079	HEK293	kidney:	embryo
11	chr12:56115029-56115079	HepG2	liver:	n/a
12	chr12:56115029-56115079	HCM	heart:	n/a
13	chr12:56115029-56115079	BE2_C	brain:	n/a
14	chr12:56115029-56115079	GM12892	blood:	n/a
15	chr12:56115029-56115079	ProgFib	skin:	n/a
16	chr12:56115029-56115079	Hela-S3	cervix:	n/a
17	chr12:56115029-56115079	NHBE	bronchial:	n/a
18	chr12:56115029-56115079	H1-hESC	embryonic stem cell:	embryo
19	chr12:56115029-56115079	Hepatocyte	liver:	n/a
20	chr12:56115029-56115079	MCF-7	breast:	n/a
21	chr12:56115029-56115079	U87	brain:	n/a
22	chr12:56115029-56115079	RPTEC	kidney:	n/a
23	chr12:56115029-56115079	HAEpiC	amniotic membrane:	n/a
24	chr12:56115029-56115079	HRCEpiC	kidney:	n/a
25	chr12:56115029-56115079	Caco-2	colon:	n/a
26	chr12:56115029-56115079	A549	lung:	n/a
27	chr12:56115029-56115079	PrEC	prostate:	n/a
28	chr12:56115029-56115079	HEEpiC	esophagus:	n/a
29	chr12:56115029-56115079	SKMC	muscle:	n/a
30	chr12:56115029-56115079	HRPEpiC	eye:	n/a
31	chr12:56115029-56115079	CMK	blood:	n/a
32	chr12:56115029-56115079	HMEC	breast:	n/a
33	chr12:56115029-56115079	AG04449	skin:	fetal
34	chr12:56115029-56115079	HCT-116	colon:	n/a
35	chr12:56115029-56115079	HNPCEpiC	eye:	n/a
36	chr12:56115029-56115079	GM12891	blood:	n/a
37	chr12:56115029-56115079	T-47D	breast:	n/a
38	chr12:56115029-56115079	AG04450	lung:	fetal
39	chr12:56115029-56115079	SK-N-MC	brain:	n/a
40	chr12:56115029-56115079	K562	blood:	n/a
41	chr12:56115029-56115079	AG10803	skin:	n/a
42	chr12:56115029-56115079	AG09319	gingival:	n/a
43	chr12:56115029-56115079	HL-60	blood:	n/a
44	chr12:56115029-56115079	NT2-D1	testis:	n/a
45	chr12:56115029-56115079	HCPEpiC	choroid plexus:	n/a
46	chr12:56115029-56115079	HRE	kidney:	n/a
47	chr12:56115029-56115079	ovcar-3	ovarian:	n/a
48	chr12:56115029-56115079	HUVEC	blood vessel:	n/a
49	chr12:56115029-56115079	GM12878	blood:	n/a
50	chr12:56115029-56115079	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56074206..56076074-chr12:56114444..56115772,12	MCF-7	breast:
2	chr12:56099897..56102707-chr12:56112712..56115453,3	K562	blood:
3	chr12:56053257..56054156-chr12:56114472..56115116,4	MCF-7	breast:
4	chr12:56073967..56077119-chr12:56108776..56115360,8	MCF-7	breast:
5	chr12:56113979..56116448-chr12:56136696..56138378,2	MCF-7	breast:
6	chr12:56115003..56117431-chr12:56512002..56513619,2	MCF-7	breast:
7	chr12:56055852..56057632-chr12:56114963..56117195,2	MCF-7	breast:
8	chr12:56048123..56050155-chr12:56113655..56116365,3	MCF-7	breast:
9	chr12:56097454..56102551-chr12:56112712..56115569,4	K562	blood:
10	chr12:56040086..56042095-chr12:56114770..56116489,2	MCF-7	breast:

Variant related genes	Relation type
RDH5	TF binding region
RDH5	CpG island
ENSG00000135414	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000272837	Chromatin interaction
ENSG00000258907	Chromatin interaction
ENSG00000270458	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000170439	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258921	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs4359251	1.00[CHD][hapmap]
rs7956337	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv525231	chr12:56076919-56124332	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
4	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 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	chr12:56109000-56115600	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr12:56111200-56115600	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr12:56111200-56115800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:56111200-56115800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:56111200-56115800	Enhancers	Right Atrium	heart
6	chr12:56111200-56120400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:56111400-56115400	Enhancers	Left Ventricle	heart
8	chr12:56111600-56115800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr12:56111600-56115800	Enhancers	HMEC	breast
10	chr12:56111600-56118400	Strong transcription	Thymus	Thymus
11	chr12:56112000-56115600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:56112000-56117800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:56112200-56115200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
14	chr12:56112200-56116600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:56112200-56118000	Weak transcription	Fetal Lung	lung
16	chr12:56112400-56115400	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr12:56112400-56115400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:56112400-56118000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:56112600-56115800	Strong transcription	Dnd41	blood
20	chr12:56112600-56117600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:56112600-56118200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:56112600-56118800	Weak transcription	Small Intestine	intestine
23	chr12:56112800-56115400	Strong transcription	Fetal Brain Female	brain
24	chr12:56112800-56115400	Enhancers	Pancreas	Pancrea
25	chr12:56112800-56115800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:56112800-56115800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:56112800-56116800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:56112800-56116800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:56112800-56117200	Strong transcription	Primary T cells from cord blood	blood
30	chr12:56112800-56120800	Weak transcription	Fetal Brain Male	brain
31	chr12:56112800-56121000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:56113000-56115200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:56113000-56115400	Enhancers	Brain Angular Gyrus	brain
34	chr12:56113000-56115400	Enhancers	Brain Cingulate Gyrus	brain
35	chr12:56113000-56115600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr12:56113000-56116600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr12:56113200-56115600	Genic enhancers	Brain Anterior Caudate	brain
38	chr12:56113200-56115600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr12:56113200-56117000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr12:56113200-56118000	Weak transcription	Ovary	ovary
41	chr12:56113200-56118600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr12:56113200-56120000	Strong transcription	Brain Germinal Matrix	brain
43	chr12:56113200-56120800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:56113400-56115200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:56113400-56115400	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr12:56113400-56115800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr12:56113400-56117200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:56113600-56115200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:56113600-56115400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:56113600-56115400	Enhancers	Brain Inferior Temporal Lobe	brain

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