Variant report

Variant	rs908511
Chromosome Location	chr12:39300741-39300742
allele	A/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	RUNX3	chr12:39300059-39301142	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:39298240-39300998	GM12878	blood:	n/a	n/a
3	ELF1	chr12:39300303-39300896	GM12878	blood:	n/a	n/a
4	CTCF	chr12:39300402-39300756	Fibrobl	skin:	n/a	chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
5	CTBP2	chr12:39298666-39300802	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZMIZ1	chr12:39300448-39300742	K562	blood:	n/a	n/a
7	ELF1	chr12:39300422-39300742	A549	lung:	n/a	n/a
8	CREB1	chr12:39300437-39300805	A549	lung:	n/a	n/a
9	SMARCC2	chr12:39298655-39300915	Hela-S3	cervix:	n/a	chr12:39298980-39298989
10	PAX5	chr12:39300374-39300807	GM12878	blood:	n/a	n/a
11	CTCF	chr12:39300408-39300749	ECC-1	luminal epithelium:	n/a	chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
12	CTCF	chr12:39300418-39300755	GM12878	blood:	n/a	chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
13	CTCF	chr12:39300386-39300753	A549	lung:	n/a	chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
14	POLR2A	chr12:39300381-39300749	A549	lung:	n/a	n/a
15	ZNF384	chr12:39300530-39300956	K562	blood:	n/a	n/a
16	TAF1	chr12:39300270-39300915	H1-hESC	embryonic stem cell:	n/a	n/a
17	EP300	chr12:39300408-39300764	SK-N-SH_RA	brain:	n/a	n/a
18	NRF1	chr12:39300410-39300777	GM12878	blood:	n/a	n/a
19	MAX	chr12:39298545-39300836	GM12878	blood:	n/a	chr12:39300641-39300651 chr12:39300127-39300137
20	POLR2A	chr12:39298411-39301114	GM19193	blood:	n/a	n/a
21	CTCF	chr12:39300335-39300781	MCF-7	breast:	n/a	chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
22	SMARCC1	chr12:39298667-39301343	Hela-S3	cervix:	n/a	chr12:39298980-39298989
23	CTCF	chr12:39300288-39300890	MCF-7	breast:	n/a	chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
24	CTCF	chr12:39300437-39300754	MCF-7	breast:	n/a	chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
25	POLR2A	chr12:39298617-39300930	GM12891	blood:	n/a	n/a
26	CTCF	chr12:39300436-39300744	MCF-7	breast:	n/a	chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
27	EBF1	chr12:39300394-39301113	GM12878	blood:	n/a	n/a
28	MAX	chr12:39300260-39300876	H1-hESC	embryonic stem cell:	n/a	chr12:39300641-39300651
29	CTCF	chr12:39300410-39300756	MCF-7	breast:	n/a	chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
30	UBTF	chr12:39300417-39300891	K562	blood:	n/a	n/a
31	SMC3	chr12:39300412-39300783	K562	blood:	n/a	chr12:39300585-39300599 chr12:39300585-39300592
32	POLR2A	chr12:39298502-39300996	GM18951	blood:	n/a	n/a
33	ELF1	chr12:39300444-39300741	HepG2	liver:	n/a	n/a
34	SMC3	chr12:39300384-39300787	HepG2	liver:	n/a	chr12:39300585-39300599 chr12:39300585-39300592
35	POLR2A	chr12:39298609-39300763	HEK293	kidney:	n/a	n/a
36	KAP1	chr12:39298516-39301267	HEK293	kidney:	n/a	n/a
37	BHLHE40	chr12:39300332-39300812	HepG2	liver:	n/a	n/a
38	CTCF	chr12:39300330-39300800	HCT-116	colon:	n/a	chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
39	HDAC2	chr12:39300429-39300787	HepG2	liver:	n/a	n/a
40	POLR2A	chr12:39298623-39300890	GM12878	blood:	n/a	n/a
41	MYC	chr12:39300367-39300762	H1-hESC	embryonic stem cell:	n/a	chr12:39300641-39300651
42	PAX5	chr12:39300262-39300951	GM12878	blood:	n/a	n/a
43	TCF12	chr12:39300453-39300756	H1-hESC	embryonic stem cell:	n/a	chr12:39300615-39300625
44	GABPA	chr12:39300424-39300749	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr12:39299503-39301028	SK-N-SH	brain:	n/a	chr12:39299584-39299597 chr12:39300586-39300595 chr12:39300584-39300600 chr12:39300583-39300601 chr12:39300588-39300598
46	EP300	chr12:39300414-39301286	GM12878	blood:	n/a	chr12:39300895-39300909
47	TCF12	chr12:39300323-39300828	A549	lung:	n/a	chr12:39300441-39300449 chr12:39300615-39300625
48	YY1	chr12:39300166-39300785	GM12878	blood:	n/a	chr12:39300313-39300324
49	YY1	chr12:39300292-39300742	A549	lung:	n/a	chr12:39300313-39300324
50	EP300	chr12:39300409-39300786	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39300010..39300760-chr3:119814285..119814942,2	Hela-S3	cervix:
2	chr12:39300444..39301044-chr12:39497356..39498030,2	K562	blood:

Variant related genes	Relation type
CPNE8	TF binding region
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1356267	0.80[JPT][hapmap]
rs1607040	0.80[JPT][hapmap]
rs1878224	0.89[ASW][hapmap];1.00[YRI][hapmap]
rs1878225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2388062	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768394	0.80[JPT][hapmap]
rs7971601	1.00[YRI][hapmap]
rs7978838	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899009	chr12:39284077-39441096	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39297000-39301200	Active TSS	Right Atrium	heart
2	chr12:39297200-39301000	Active TSS	Brain Hippocampus Middle	brain
3	chr12:39297200-39301000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:39297200-39301000	Active TSS	K562	blood
5	chr12:39297200-39301200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr12:39297400-39301000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr12:39297600-39300800	Active TSS	Brain Anterior Caudate	brain
8	chr12:39297600-39301000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:39297600-39301400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:39297600-39301400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:39297800-39301000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:39297800-39301200	Active TSS	Brain Angular Gyrus	brain
13	chr12:39297800-39301200	Active TSS	Brain Cingulate Gyrus	brain
14	chr12:39297800-39301400	Active TSS	GM12878-XiMat	blood
15	chr12:39298000-39300800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr12:39298000-39300800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:39298000-39300800	Active TSS	Lung	lung
18	chr12:39298000-39301000	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr12:39298000-39301000	Active TSS	Duodenum Mucosa	Duodenum
20	chr12:39298000-39301200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:39298000-39301400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr12:39298200-39300800	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr12:39298200-39300800	Active TSS	Rectal Smooth Muscle	rectum
24	chr12:39298200-39301000	Active TSS	Colon Smooth Muscle	Colon
25	chr12:39298200-39301000	Active TSS	Left Ventricle	heart
26	chr12:39298200-39301000	Active TSS	A549	lung
27	chr12:39298200-39301000	Active TSS	Hela-S3	cervix
28	chr12:39298200-39301200	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr12:39298200-39301200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:39298200-39301200	Active TSS	Muscle Satellite Cultured Cells	--
31	chr12:39298200-39301200	Active TSS	HMEC	breast
32	chr12:39298200-39301400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:39298200-39301400	Active TSS	Right Ventricle	heart
34	chr12:39298200-39301400	Active TSS	NHDF-Ad	bronchial
35	chr12:39298400-39300800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:39298400-39300800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:39298400-39300800	Active TSS	Liver	Liver
38	chr12:39298400-39300800	Active TSS	Esophagus	oesophagus
39	chr12:39298400-39301000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:39298400-39301000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr12:39298400-39301000	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:39298400-39301000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:39298400-39301000	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr12:39298400-39301000	Active TSS	Fetal Intestine Small	intestine
45	chr12:39298400-39301000	Active TSS	Stomach Mucosa	stomach
46	chr12:39298400-39301200	Active TSS	Fetal Intestine Large	intestine
47	chr12:39298400-39301400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:39298600-39301000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:39298600-39301000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:39298600-39301000	Active TSS	Aorta	Aorta

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