Variant report

Variant	rs12076680
Chromosome Location	chr1:46647893-46647894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:46647053-46647960	MCF-7	breast:	n/a	chr1:46647651-46647659
2	EP300	chr1:46646992-46648026	ECC-1	luminal epithelium:	n/a	n/a
3	GATA3	chr1:46647049-46648084	SK-N-SH	brain:	n/a	chr1:46647651-46647659
4	ZNF384	chr1:46647877-46648119	GM12878	blood:	n/a	n/a
5	GATA3	chr1:46647220-46648032	SK-N-SH	brain:	n/a	chr1:46647651-46647659
6	TCF12	chr1:46647177-46648024	ECC-1	luminal epithelium:	n/a	n/a
7	GATA3	chr1:46647138-46647962	MCF-7	breast:	n/a	chr1:46647651-46647659
8	TCF12	chr1:46647122-46648023	ECC-1	luminal epithelium:	n/a	n/a
9	ZNF384	chr1:46647813-46648144	K562	blood:	n/a	n/a
10	NFIC	chr1:46647136-46647908	ECC-1	luminal epithelium:	n/a	n/a
11	TCF12	chr1:46647130-46648155	SK-N-SH	brain:	n/a	n/a
12	MAX	chr1:46647216-46647906	ECC-1	luminal epithelium:	n/a	n/a
13	TCF12	chr1:46647204-46647985	SK-N-SH	brain:	n/a	n/a
14	GATA2	chr1:46647216-46647905	HUVEC	blood vessel:	n/a	chr1:46647651-46647659
15	EP300	chr1:46646993-46647981	SK-N-SH	brain:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46596322..46599867-chr1:46644378..46648277,6	K562	blood:
2	chr1:46592691..46601867-chr1:46642778..46650670,25	MCF-7	breast:
3	chr1:46644247..46646808-chr1:46647316..46649049,2	MCF-7	breast:
4	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
5	chr1:46634262..46636688-chr1:46646311..46648808,2	MCF-7	breast:
6	chr1:46646789..46649181-chr1:46713269..46714809,2	K562	blood:
7	chr1:46535067..46536956-chr1:46646788..46648510,2	K562	blood:
8	chr1:46534589..46536956-chr1:46645759..46648288,3	K562	blood:
9	chr1:46636220..46637897-chr1:46645659..46648862,3	MCF-7	breast:
10	chr1:46638980..46642595-chr1:46645721..46649189,9	MCF-7	breast:
11	chr1:46645973..46650649-chr1:46685566..46691437,5	MCF-7	breast:

No data

Variant related genes	Relation type
TSPAN1	TF binding region
ENSG00000227857	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000250719	Chromatin interaction
ENSG00000117472	Chromatin interaction
ENSG00000085998	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12123115	1.00[ASN][1000 genomes]
rs55884940	1.00[ASN][1000 genomes]
rs72677567	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers 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 target site	72 gene(s)	inside rSNPs	diseases
4	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12076680	CCDC163P,LOC126661	cis	brain	BrainEAC
rs12076680	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs12076680	CCDC163P	cis	lung	GTEx
rs12076680	CCDC163P	cis	Esophagus Muscularis	GTEx
rs12076680	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs12076680	CCDC163P,LOC126661	cis	frontal cortex	BrainEAC
rs12076680	CCDC163P,LOC126661	cis	cerebellar cortex	BrainEAC
rs12076680	CCDC163P	cis	Whole Blood	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46637800-46649600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:46639400-46653800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:46639600-46652800	Weak transcription	Brain Germinal Matrix	brain
4	chr1:46640600-46648800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:46640800-46656400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:46641000-46648600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:46641200-46648800	Weak transcription	HSMMtube	muscle
8	chr1:46641200-46649000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:46641400-46648600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:46642200-46648400	Weak transcription	Left Ventricle	heart
11	chr1:46642400-46648800	Weak transcription	Right Atrium	heart
12	chr1:46642400-46648800	Weak transcription	Right Ventricle	heart
13	chr1:46644400-46648400	Weak transcription	Psoas Muscle	Psoas
14	chr1:46644800-46651400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:46645000-46648000	Flanking Active TSS	Hela-S3	cervix
16	chr1:46645000-46651400	Enhancers	Fetal Thymus	thymus
17	chr1:46645200-46648800	Active TSS	Rectal Smooth Muscle	rectum
18	chr1:46645200-46649800	Enhancers	Placenta	Placenta
19	chr1:46645200-46650200	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:46645200-46651400	Enhancers	Pancreas	Pancrea
21	chr1:46645200-46657800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:46645400-46648800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:46645400-46649000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:46645400-46649200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:46645400-46649600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:46645400-46650600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:46645400-46652200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:46645600-46648000	Flanking Active TSS	HMEC	breast
29	chr1:46645600-46648400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:46645600-46648800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:46645600-46649000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:46645600-46649200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:46645600-46649600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:46645600-46650400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:46645600-46650400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:46645600-46650800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:46645600-46652800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:46645600-46653200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:46645600-46653600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:46645600-46658200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:46645800-46648000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:46645800-46648800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:46645800-46663200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr1:46646000-46648400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:46646000-46648800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:46646000-46649200	Active TSS	Colonic Mucosa	Colon
47	chr1:46646000-46652800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:46646000-46653200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:46646000-46654400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:46646000-46657600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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