Variant report

Variant	rs58164425
Chromosome Location	chr3:112933234-112933235
allele	A/C
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	ESR1	chr3:112933135-112933391	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr3:112933200-112933350	AG10803	skin:	n/a	n/a
3	CTCF	chr3:112933200-112933350	HEK293	kidney:	n/a	n/a
4	CTCF	chr3:112933160-112933310	NHEK	skin:	n/a	n/a
5	CTCF	chr3:112933140-112933290	GM12864	blood:	n/a	n/a
6	CTCF	chr3:112933200-112933350	NHDF-neo	bronchial:	n/a	n/a
7	CTCF	chr3:112933200-112933350	HAc	cerebellar:	n/a	n/a
8	RAD21	chr3:112933034-112933484	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:112933120-112933270	HMF	breast:	n/a	n/a
10	ESR1	chr3:112933074-112933413	ECC-1	luminal epithelium:	n/a	n/a
11	CTCF	chr3:112933220-112933370	GM12871	blood:	n/a	n/a
12	CTCF	chr3:112933120-112933270	GM12873	blood:	n/a	n/a
13	CTCF	chr3:112933140-112933290	AG09319	gingival:	n/a	n/a
14	CTCF	chr3:112933160-112933310	AG04449	skin:	n/a	n/a

Variant related genes	Relation type
BOC	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12636333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638736	1.00[EUR][1000 genomes];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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877346	chr3:112893640-112938683	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv877347	chr3:112895679-112934752	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112929600-112934200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:112931200-112933800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr3:112931600-112933400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
4	chr3:112931800-112933400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr3:112931800-112933600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:112931800-112950800	Weak transcription	Lung	lung
7	chr3:112932000-112933600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
8	chr3:112932000-112937200	Weak transcription	Psoas Muscle	Psoas
9	chr3:112932000-112972800	Weak transcription	Aorta	Aorta
10	chr3:112932200-112933400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:112932200-112933400	Flanking Active TSS	Colon Smooth Muscle	Colon
12	chr3:112932200-112933400	Active TSS	Fetal Muscle Trunk	muscle
13	chr3:112932200-112933400	Weak transcription	A549	lung
14	chr3:112932200-112933600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:112932200-112933800	Weak transcription	HSMM	muscle
16	chr3:112932200-112934000	Weak transcription	HSMMtube	muscle
17	chr3:112932200-112934200	Enhancers	NH-A	brain
18	chr3:112932200-112934600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:112932200-112935000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:112932200-112942600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:112932400-112933400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:112932400-112933400	Flanking Active TSS	NHDF-Ad	bronchial
23	chr3:112932400-112933600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:112932400-112934400	Enhancers	Fetal Kidney	kidney
25	chr3:112932400-112935000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:112932400-112935000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:112932400-112935000	Weak transcription	Ovary	ovary
28	chr3:112932400-112937200	Weak transcription	Brain Substantia Nigra	brain
29	chr3:112932400-112937400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:112932400-112941200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:112932600-112933600	Weak transcription	Osteobl	bone
32	chr3:112932600-112934600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:112932600-112934600	Enhancers	NHEK	skin
34	chr3:112932600-112942600	Weak transcription	NHLF	lung
35	chr3:112932800-112933600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:112932800-112933800	Active TSS	Fetal Brain Female	brain
37	chr3:112932800-112934000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:112932800-112934400	Active TSS	Stomach Smooth Muscle	stomach
39	chr3:112933000-112933400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr3:112933000-112933400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:112933000-112933400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr3:112933000-112933400	Enhancers	Fetal Lung	lung
43	chr3:112933000-112934000	Weak transcription	HMEC	breast
44	chr3:112933000-112934800	Enhancers	Fetal Stomach	stomach
45	chr3:112933000-112935000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:112933000-112935200	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:112933000-112935800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:112933000-112936600	Weak transcription	Pancreas	Pancrea
49	chr3:112933000-112937600	Weak transcription	Esophagus	oesophagus
50	chr3:112933000-112940200	Weak transcription	Brain Germinal Matrix	brain

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