Variant report

Variant	rs12495847
Chromosome Location	chr3:134090505-134090506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:103)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:103 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:134086773-134094473	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr3:134090420-134090570	AG04450	lung:	n/a	n/a
3	TEAD4	chr3:134090369-134090794	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr3:134090360-134090510	HEEpiC	esophagus:	n/a	n/a
5	TCF12	chr3:134089251-134090568	ECC-1	luminal epithelium:	n/a	n/a
6	CTCF	chr3:134090420-134090570	HRPEpiC	eye:	n/a	n/a
7	CTCF	chr3:134090360-134090510	HEK293	kidney:	n/a	n/a
8	POLR2A	chr3:134086772-134094312	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr3:134090400-134090550	NHDF-neo	bronchial:	n/a	n/a
10	TEAD4	chr3:134089522-134090875	ECC-1	luminal epithelium:	n/a	n/a
11	CTCF	chr3:134090380-134090530	HFF	foreskin:	n/a	n/a
12	POLR2A	chr3:134090007-134090583	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr3:134086769-134091751	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr3:134090169-134090812	HCT-116	colon:	n/a	n/a
15	CTCF	chr3:134090440-134090590	HPAF	blood vessel:	n/a	n/a
16	CTCF	chr3:134090380-134090530	AG04449	skin:	n/a	n/a
17	TEAD4	chr3:134090413-134090697	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr3:134090400-134090550	HCM	heart:	n/a	n/a
19	POLR2A	chr3:134090064-134093861	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr3:134090460-134090610	HBMEC	blood vessel:	n/a	n/a
21	POLR2A	chr3:134079921-134092871	ECC-1	luminal epithelium:	n/a	n/a
22	CTCF	chr3:134090440-134090590	SAEC	small airway:	n/a	n/a
23	CTCF	chr3:134090420-134090570	HMF	breast:	n/a	n/a
24	CTCF	chr3:134090420-134090570	HFF-Myc	foreskin:	n/a	n/a
25	CTCF	chr3:134090380-134090530	SK-N-SH_RA	brain:	n/a	n/a
26	CTCF	chr3:134090420-134090570	HVMF	connective:	n/a	n/a
27	CTCF	chr3:134090440-134090590	HBMEC	blood vessel:	n/a	n/a
28	CTCF	chr3:134090400-134090550	HMEC	breast:	n/a	n/a
29	CTCF	chr3:134090400-134090550	HEEpiC	esophagus:	n/a	n/a
30	CTCF	chr3:134090420-134090570	HPAF	blood vessel:	n/a	n/a
31	CTCF	chr3:134090400-134090550	AG10803	skin:	n/a	n/a
32	CTCF	chr3:134090420-134090570	WERI-Rb-1	eye:	n/a	n/a
33	CTCF	chr3:134090380-134090530	AoAF	blood vessel:	n/a	n/a
34	RAD21	chr3:134090267-134090658	A549	lung:	n/a	n/a
35	CTCF	chr3:134090460-134090610	HCPEpiC	choroid plexus:	n/a	n/a
36	CTCF	chr3:134090420-134090570	HMEC	breast:	n/a	n/a
37	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
38	RAD21	chr3:134090392-134090558	SK-N-SH_RA	brain:	n/a	n/a
39	POLR2A	chr3:134089460-134093902	ProgFib	skin:	n/a	n/a
40	POLR2A	chr3:134088558-134094000	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr3:134090500-134090650	AG09319	gingival:	n/a	n/a
42	CTCF	chr3:134090439-134090578	MCF-7	breast:	n/a	n/a
43	POLR2A	chr3:134090496-134090681	MCF10A-Er-Src	breast:	n/a	n/a
44	CTCF	chr3:134090460-134090610	HRPEpiC	eye:	n/a	n/a
45	CTCF	chr3:134090420-134090570	HCPEpiC	choroid plexus:	n/a	n/a
46	POLR2A	chr3:134089143-134090554	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAZ	chr3:134090327-134090584	HepG2	liver:	n/a	n/a
48	CTCF	chr3:134090290-134090587	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr3:134071087-134094366	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr3:134090395-134090586	NHEK	skin:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:134090463-134090513	HNPCEpiC	eye:	n/a
2	chr3:134090463-134090513	HRPEpiC	eye:	n/a
3	chr3:134090463-134090513	AG09309	skin:	n/a
4	chr3:134090463-134090513	AoSMC	blood vessel:	n/a
5	chr3:134090463-134090513	PFSK-1	brain:	n/a
6	chr3:134090463-134090513	BJ	skin:	n/a
7	chr3:134090463-134090513	PrEC	prostate:	n/a
8	chr3:134090463-134090513	HPAEpiC	pulmonary alveolar:	n/a
9	chr3:134090463-134090513	HepG2	liver:	n/a
10	chr3:134090463-134090513	SK-N-SH	brain:	n/a
11	chr3:134090463-134090513	SK-N-MC	brain:	n/a
12	chr3:134090463-134090513	ovcar-3	ovarian:	n/a
13	chr3:134090463-134090513	AG10803	skin:	n/a
14	chr3:134090463-134090513	PANC-1	pancreas:	n/a
15	chr3:134090463-134090513	NB4	blood:	n/a
16	chr3:134090463-134090513	GM06990	blood:	n/a
17	chr3:134090463-134090513	GM12892	blood:	n/a
18	chr3:134090463-134090513	HL-60	blood:	n/a
19	chr3:134090463-134090513	Hepatocyte	liver:	n/a
20	chr3:134090463-134090513	RPTEC	kidney:	n/a
21	chr3:134090463-134090513	NHDF-neo	bronchial:	n/a
22	chr3:134090463-134090513	HCF	heart:	n/a
23	chr3:134090463-134090513	AG04450	lung:	fetal
24	chr3:134090463-134090513	BE2_C	brain:	n/a
25	chr3:134090463-134090513	HEEpiC	esophagus:	n/a
26	chr3:134090463-134090513	CMK	blood:	n/a
27	chr3:134090463-134090513	HUVEC	blood vessel:	n/a
28	chr3:134090463-134090513	HCM	heart:	n/a
29	chr3:134090463-134090513	AG04449	skin:	fetal
30	chr3:134090463-134090513	HRE	kidney:	n/a
31	chr3:134090463-134090513	GM12891	blood:	n/a
32	chr3:134090463-134090513	AG09319	gingival:	n/a
33	chr3:134090463-134090513	NHBE	bronchial:	n/a
34	chr3:134090463-134090513	SK-N-SH_RA	brain:	n/a
35	chr3:134090463-134090513	SKMC	muscle:	n/a
36	chr3:134090463-134090513	MCF10A-Er-Src	breast:	n/a
37	chr3:134090463-134090513	SAEC	small airway:	n/a
38	chr3:134090463-134090513	HCPEpiC	choroid plexus:	n/a
39	chr3:134090463-134090513	HRCEpiC	kidney:	n/a
40	chr3:134090463-134090513	HCT-116	colon:	n/a
41	chr3:134090463-134090513	H1-hESC	embryonic stem cell:	embryo
42	chr3:134090463-134090513	ECC-1	luminal epithelium:	n/a
43	chr3:134090463-134090513	Caco-2	colon:	n/a
44	chr3:134090463-134090513	NT2-D1	testis:	n/a
45	chr3:134090463-134090513	LNCaP	prostate:	n/a
46	chr3:134090463-134090513	Jurkat	blood:	n/a
47	chr3:134090463-134090513	GM12878	blood:	n/a
48	chr3:134090463-134090513	MCF-7	breast:	n/a
49	chr3:134090463-134090513	HEK293	kidney:	embryo
50	chr3:134090463-134090513	GM19239	blood:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:65587328..65588998-chr3:134088720..134091228,2	MCF-7	breast:
2	chr3:134089711..134094738-chr3:134202793..134208651,12	MCF-7	breast:
3	chr3:134088513..134090670-chr3:134202768..134204807,2	MCF-7	breast:
4	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
5	chr3:134032463..134034261-chr3:134088924..134090604,2	K562	blood:
6	chr3:134026968..134027634-chr3:134090071..134090721,3	MCF-7	breast:

No data

Variant related genes	Relation type
AMOTL2	TF binding region
AMOTL2	CpG island
ENSG00000182923	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000240006	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10755085	0.96[ASN][1000 genomes]
rs10755086	0.96[ASN][1000 genomes]
rs11708815	0.85[ASN][1000 genomes]
rs11719057	0.85[ASN][1000 genomes]
rs12496438	0.96[ASN][1000 genomes]
rs13075185	0.85[ASN][1000 genomes]
rs13322269	1.00[ASN][1000 genomes]
rs1353776	0.80[ASN][1000 genomes]
rs1353777	1.00[ASN][1000 genomes]
rs1353778	0.96[ASN][1000 genomes]
rs1466827	0.89[ASN][1000 genomes]
rs1863910	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732852	0.80[ASN][1000 genomes]
rs3755762	0.96[ASN][1000 genomes]
rs3773820	0.85[ASN][1000 genomes]
rs3821705	0.80[ASN][1000 genomes]
rs4264700	0.80[ASN][1000 genomes]
rs4974489	0.80[ASN][1000 genomes]
rs4974491	0.80[ASN][1000 genomes]
rs4974498	0.80[ASN][1000 genomes]
rs6439478	0.80[ASN][1000 genomes]
rs6786148	0.80[ASN][1000 genomes]
rs7613066	0.85[ASN][1000 genomes]
rs9817900	0.80[ASN][1000 genomes]
rs9853621	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers 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 miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134072400-134091200	Genic enhancers	Spleen	Spleen
2	chr3:134072800-134090600	Genic enhancers	Left Ventricle	heart
3	chr3:134073400-134091400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:134081400-134090600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:134081600-134091000	Enhancers	Psoas Muscle	Psoas
6	chr3:134082000-134090800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:134082000-134090800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:134082000-134091000	Genic enhancers	Fetal Stomach	stomach
9	chr3:134082200-134092800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:134082400-134091400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:134083600-134090800	Genic enhancers	Fetal Intestine Large	intestine
12	chr3:134084000-134090800	Genic enhancers	Lung	lung
13	chr3:134084600-134090800	Genic enhancers	Aorta	Aorta
14	chr3:134085800-134090800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:134086000-134091000	Genic enhancers	HepG2	liver
16	chr3:134086800-134090600	Genic enhancers	Fetal Intestine Small	intestine
17	chr3:134087200-134092600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:134087400-134091600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr3:134087600-134091200	Genic enhancers	Fetal Lung	lung
20	chr3:134087600-134091400	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
21	chr3:134087600-134092400	Transcr. at gene 5' and 3'	A549	lung
22	chr3:134087800-134091600	Transcr. at gene 5' and 3'	HSMM	muscle
23	chr3:134087800-134091800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
24	chr3:134087800-134092600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
25	chr3:134087800-134092600	Transcr. at gene 5' and 3'	Osteobl	bone
26	chr3:134088000-134090800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:134088000-134091000	Transcr. at gene 5' and 3'	NH-A	brain
28	chr3:134088000-134091400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:134088000-134091600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
30	chr3:134088200-134092600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:134088400-134091200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:134088400-134092200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:134088400-134092600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:134088600-134090600	Genic enhancers	Colonic Mucosa	Colon
35	chr3:134088600-134091400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
36	chr3:134088600-134091600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
37	chr3:134088600-134092400	Transcr. at gene 5' and 3'	NHLF	lung
38	chr3:134088800-134091000	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:134088800-134091200	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
40	chr3:134088800-134091200	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
41	chr3:134088800-134091600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:134089000-134091000	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:134089200-134090600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:134089200-134090600	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
45	chr3:134089200-134092600	Transcr. at gene 5' and 3'	NHEK	skin
46	chr3:134089400-134090800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:134089400-134090800	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
48	chr3:134089400-134091000	Genic enhancers	H1 Cell Line	embryonic stem cell
49	chr3:134089400-134091000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:134089400-134091200	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain

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