Variant report

Variant	rs12496438
Chromosome Location	chr3:134094341-134094342
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	MAX	chr3:134092873-134094398	HCT-116	colon:	n/a	chr3:134093443-134093453
2	POLR2A	chr3:134086773-134094473	Hela-S3	cervix:	n/a	n/a
3	MAFK	chr3:134093122-134094465	Hela-S3	cervix:	n/a	n/a
4	TBP	chr3:134093097-134094431	Hela-S3	cervix:	n/a	n/a
5	ZBTB7A	chr3:134093144-134094694	ECC-1	luminal epithelium:	n/a	n/a
6	HDAC2	chr3:134092846-134094356	MCF-7	breast:	n/a	n/a
7	EP300	chr3:134091790-134094514	ECC-1	luminal epithelium:	n/a	chr3:134093458-134093467 chr3:134091915-134091931 chr3:134092363-134092379 chr3:134092748-134092757
8	ELK1	chr3:134093073-134094381	Hela-S3	cervix:	n/a	n/a
9	MXI1	chr3:134093041-134094376	Hela-S3	cervix:	n/a	n/a
10	RCOR1	chr3:134091947-134094409	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:134091825-134094472	Hela-S3	cervix:	n/a	n/a
12	EP300	chr3:134092297-134094402	ECC-1	luminal epithelium:	n/a	chr3:134093458-134093467 chr3:134092363-134092379 chr3:134092748-134092757
13	RFX5	chr3:134091836-134094520	Hela-S3	cervix:	n/a	n/a
14	TEAD4	chr3:134091947-134094381	ECC-1	luminal epithelium:	n/a	n/a
15	TCF12	chr3:134091783-134094382	ECC-1	luminal epithelium:	n/a	chr3:134092197-134092205 chr3:134093938-134093947 chr3:134091915-134091925
16	CEBPB	chr3:134092476-134094394	Hela-S3	cervix:	n/a	n/a
17	GTF2F1	chr3:134093088-134094494	Hela-S3	cervix:	n/a	n/a
18	TAF1	chr3:134091772-134094474	H1-hESC	embryonic stem cell:	n/a	n/a
19	BACH1	chr3:134093276-134094413	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr3:134093003-134094417	ECC-1	luminal epithelium:	n/a	chr3:134093425-134093437 chr3:134093415-134093427
21	TCF7L2	chr3:134092974-134094381	HEK293	kidney:	n/a	chr3:134093922-134093929 chr3:134093379-134093393
22	SMC3	chr3:134091260-134094465	Hela-S3	cervix:	n/a	n/a
23	ESR1	chr3:134092903-134094429	ECC-1	luminal epithelium:	n/a	chr3:134094008-134094023
24	BRCA1	chr3:134092282-134094562	Hela-S3	cervix:	n/a	n/a
25	NFIC	chr3:134092260-134094344	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr3:134091780-134094364	PANC-1	pancreas:	n/a	n/a
27	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
28	SIN3A	chr3:134091883-134094577	H1-hESC	embryonic stem cell:	n/a	chr3:134093487-134093500 chr3:134093529-134093542
29	TFAP2C	chr3:134092025-134094581	Hela-S3	cervix:	n/a	chr3:134092572-134092587 chr3:134093979-134093988 chr3:134092550-134092565 chr3:134093841-134093856
30	ESR1	chr3:134092913-134094352	ECC-1	luminal epithelium:	n/a	chr3:134094008-134094023
31	SP1	chr3:134093021-134094355	A549	lung:	n/a	chr3:134093461-134093475 chr3:134093431-134093445 chr3:134093565-134093578 chr3:134093424-134093438 chr3:134093447-134093461
32	MAX	chr3:134091984-134094458	H1-hESC	embryonic stem cell:	n/a	chr3:134092343-134092353 chr3:134093443-134093453
33	TAF1	chr3:134092000-134094372	ECC-1	luminal epithelium:	n/a	n/a
34	TEAD4	chr3:134091666-134094419	ECC-1	luminal epithelium:	n/a	chr3:134091797-134091806
35	GATA3	chr3:134091971-134094399	A549	lung:	n/a	chr3:134092098-134092107
36	NR3C1	chr3:134093037-134094343	A549	lung:	n/a	n/a
37	FOXM1	chr3:134092123-134094448	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr3:134071087-134094366	Hela-S3	cervix:	n/a	n/a
39	EP300	chr3:134093057-134094373	MCF-7	breast:	n/a	chr3:134093458-134093467
40	CTCF	chr3:134094220-134094370	GM12867	blood:	n/a	n/a
41	MAX	chr3:134092897-134094350	ECC-1	luminal epithelium:	n/a	chr3:134093443-134093453
42	MAX	chr3:134091777-134094489	A549	lung:	n/a	chr3:134092343-134092353 chr3:134093443-134093453
43	ZKSCAN1	chr3:134093081-134094380	Hela-S3	cervix:	n/a	n/a
44	HA-E2F1	chr3:134092990-134094360	Hela-S3	cervix:	n/a	chr3:134093439-134093451 chr3:134093293-134093304
45	MAX	chr3:134092892-134094452	MCF-7	breast:	n/a	chr3:134093443-134093453
46	GATA3	chr3:134092258-134094413	MCF-7	breast:	n/a	n/a
47	NFIC	chr3:134092074-134094488	ECC-1	luminal epithelium:	n/a	n/a
48	SMARCC1	chr3:134091584-134094501	Hela-S3	cervix:	n/a	n/a
49	MAZ	chr3:134085077-134094456	IMR90	lung:	n/a	chr3:134092343-134092353 chr3:134093443-134093453 chr3:134087585-134087594
50	TCF7L2	chr3:134092913-134094409	PANC-1	pancreas:	n/a	chr3:134093922-134093929 chr3:134093379-134093393

No.	Distal block	Cell Line	Cell type
1	chr3:134091805..134100491-chr3:134198620..134206897,15	MCF-7	breast:
2	chr3:134089711..134094738-chr3:134202793..134208651,12	MCF-7	breast:
3	chr3:133968058..133969986-chr3:134093152..134094854,2	MCF-7	breast:
4	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:

Variant related genes	Relation type
AMOTL2	TF binding region
ENSG00000182923	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000163785	Chromatin interaction
ENSG00000240006	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10755085	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10755086	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708815	0.89[ASN][1000 genomes]
rs12495847	0.96[ASN][1000 genomes]
rs13075185	0.89[ASN][1000 genomes]
rs13322269	0.96[ASN][1000 genomes]
rs1353776	0.84[ASN][1000 genomes]
rs1353777	0.96[ASN][1000 genomes]
rs1353778	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466827	0.84[ASN][1000 genomes]
rs1863910	0.96[ASN][1000 genomes]
rs2303635	0.82[ASN][1000 genomes]
rs3732852	0.84[ASN][1000 genomes]
rs3755762	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773820	0.89[ASN][1000 genomes]
rs3821705	0.84[ASN][1000 genomes]
rs4974498	0.84[ASN][1000 genomes]
rs6439478	0.84[ASN][1000 genomes]
rs7613066	0.89[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12496438	RP11-375I20.6	cis	Thyroid	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134090400-134094400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr3:134091400-134094400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:134091600-134094400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr3:134091800-134094400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr3:134091800-134094600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:134092200-134094400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:134092600-134094400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:134092600-134094600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr3:134093400-134094400	Flanking Active TSS	HMEC	breast
10	chr3:134093400-134094600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:134093400-134094600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:134093400-134094600	Flanking Active TSS	Colonic Mucosa	Colon
13	chr3:134093600-134094400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:134093600-134094400	Flanking Active TSS	Rectal Smooth Muscle	rectum
15	chr3:134093600-134094400	Flanking Active TSS	HUVEC	blood vessel
16	chr3:134093600-134094400	Flanking Active TSS	NH-A	brain
17	chr3:134093600-134094600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
18	chr3:134093600-134094600	Flanking Active TSS	Fetal Heart	heart
19	chr3:134093600-134094600	Flanking Active TSS	Fetal Intestine Small	intestine
20	chr3:134093600-134094600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr3:134093600-134094600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr3:134093600-134094600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr3:134093600-134094600	Flanking Active TSS	NHEK	skin
24	chr3:134093600-134094800	Flanking Active TSS	Hela-S3	cervix
25	chr3:134093600-134095000	Flanking Bivalent TSS/Enh	HepG2	liver
26	chr3:134093600-134095200	Flanking Active TSS	Liver	Liver
27	chr3:134093600-134095600	Enhancers	Small Intestine	intestine
28	chr3:134093800-134094400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:134093800-134094400	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr3:134093800-134094400	Bivalent Enhancer	Fetal Thymus	thymus
31	chr3:134093800-134094400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
32	chr3:134093800-134094600	Flanking Active TSS	Fetal Intestine Large	intestine
33	chr3:134094000-134094400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
34	chr3:134094000-134094400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr3:134094000-134094400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr3:134094000-134094400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:134094000-134094400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
38	chr3:134094000-134094400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
39	chr3:134094000-134094400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
40	chr3:134094000-134094400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:134094000-134094400	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr3:134094000-134094400	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr3:134094000-134094400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:134094000-134094400	Flanking Active TSS	Pancreas	Pancrea
45	chr3:134094000-134094400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
46	chr3:134094000-134094400	Flanking Active TSS	Right Ventricle	heart
47	chr3:134094000-134094600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:134094000-134094600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:134094000-134094600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:134094000-134094600	Enhancers	Fetal Brain Male	brain

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