Variant report

Variant	rs1353778
Chromosome Location	chr3:134088443-134088444
allele	A/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	POLR2A	chr3:134086773-134094473	Hela-S3	cervix:	n/a	n/a
2	TCF12	chr3:134087810-134088828	SK-N-SH	brain:	n/a	chr3:134088522-134088531
3	POLR2A	chr3:134086779-134088527	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:134086772-134094312	ECC-1	luminal epithelium:	n/a	n/a
5	NFIC	chr3:134087826-134088633	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:134086769-134091751	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:134086781-134089740	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr3:134087689-134088607	U87	brain:	n/a	n/a
9	FOS	chr3:134087940-134088639	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr3:134086746-134088516	H1-hESC	embryonic stem cell:	n/a	n/a
11	GATA2	chr3:134087959-134089469	HUVEC	blood vessel:	n/a	chr3:134089000-134089010
12	POLR2A	chr3:134079921-134092871	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr3:134087982-134088625	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:134081387-134089755	HUVEC	blood vessel:	n/a	n/a
15	PBX3	chr3:134087933-134088698	SK-N-SH	brain:	n/a	chr3:134088472-134088481
16	FOSL2	chr3:134087874-134088488	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr3:134088093-134088512	T-47D	breast:	n/a	n/a
18	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
19	GATA3	chr3:134088082-134088514	T-47D	breast:	n/a	n/a
20	POLR2A	chr3:134081290-134088706	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr3:134088327-134088474	HUVEC	blood vessel:	n/a	n/a
22	PBX3	chr3:134087903-134088765	SK-N-SH	brain:	n/a	chr3:134088472-134088481
23	CTCF	chr3:134088360-134088510	AG10803	skin:	n/a	n/a
24	CTCF	chr3:134088440-134088590	HCFaa	heart:	n/a	chr3:134088575-134088584
25	GATA3	chr3:134087807-134088754	SK-N-SH	brain:	n/a	n/a
26	JUN	chr3:134087997-134088572	HUVEC	blood vessel:	n/a	n/a
27	SIN3AK20	chr3:134088022-134088472	SK-N-SH	brain:	n/a	n/a
28	CTCF	chr3:134088380-134088530	HPAF	blood vessel:	n/a	n/a
29	EP300	chr3:134087815-134088611	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr3:134071087-134094366	Hela-S3	cervix:	n/a	n/a
31	USF2	chr3:134088047-134089825	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr3:134088340-134088490	AG04449	skin:	n/a	n/a
33	POLR2A	chr3:134084882-134093800	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr3:134071303-134093679	HepG2	liver:	n/a	n/a
35	POLR2A	chr3:134086789-134089780	HUVEC	blood vessel:	n/a	n/a
36	CTCF	chr3:134088320-134088470	WERI-Rb-1	eye:	n/a	n/a
37	POLR2A	chr3:134086770-134089017	SK-N-SH	brain:	n/a	n/a
38	TCF12	chr3:134087957-134088765	A549	lung:	n/a	chr3:134088522-134088531
39	MAZ	chr3:134085077-134094456	IMR90	lung:	n/a	chr3:134092343-134092353 chr3:134093443-134093453 chr3:134087585-134087594
40	CTCF	chr3:134088320-134088470	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr3:134074967-134094367	PANC-1	pancreas:	n/a	n/a
42	POLR2A	chr3:134080043-134092973	A549	lung:	n/a	n/a
43	MAX	chr3:134088046-134088657	A549	lung:	n/a	n/a
44	POLR2A	chr3:134080609-134094580	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr3:134085086-134089605	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr3:134079902-134094732	H1-hESC	embryonic stem cell:	n/a	n/a
47	GATA3	chr3:134087928-134088727	SK-N-SH	brain:	n/a	n/a
48	TEAD4	chr3:134087825-134088649	SK-N-SH	brain:	n/a	n/a
49	MAX	chr3:134087985-134088495	SK-N-SH	brain:	n/a	n/a
50	CTCF	chr3:134088300-134088450	AoAF	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:134085828..134088665-chr3:134170796..134172844,2	MCF-7	breast:
2	chr3:134087277..134089419-chr3:134195150..134197422,2	MCF-7	breast:
3	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
4	chr3:134086152..134088581-chr3:134189583..134191121,2	MCF-7	breast:
5	chr3:134087226..134089802-chr3:134191337..134194305,2	MCF-7	breast:

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

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10755085	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10755086	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1111516	1.00[CHB][hapmap]
rs11708815	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11719057	0.89[CHB][hapmap]
rs12495847	0.96[ASN][1000 genomes]
rs12496438	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075185	0.89[ASN][1000 genomes]
rs13322269	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1353776	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1353777	0.96[ASN][1000 genomes]
rs1466827	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs1863910	0.96[ASN][1000 genomes]
rs2303635	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs2400278	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs2400279	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[AMR][1000 genomes]
rs3732852	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3755762	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773820	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3821705	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4264700	0.89[CHB][hapmap]
rs4974494	1.00[CHB][hapmap]
rs4974495	1.00[CHB][hapmap]
rs4974496	1.00[CHB][hapmap]
rs4974497	0.82[AMR][1000 genomes]
rs4974498	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6439477	1.00[CHB][hapmap]
rs6439478	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7613066	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9450	0.81[AMR][1000 genomes]
rs9853621	0.89[CHB][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1353778	RP11-375I20.6	cis	Thyroid	GTEx
rs1353778	TMEM22	cis	parietal	SCAN
rs1353778	COPB2	cis	cerebellum	SCAN
rs1353778	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs1353778	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs1353778	SLCO2A1	cis	lesional skin	skin_eQTL
rs1353778	RBP1	cis	parietal	SCAN
rs1353778	RP11-375I20.6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134069200-134090000	Genic enhancers	Fetal Muscle Trunk	muscle
2	chr3:134069400-134089800	Genic enhancers	Fetal Muscle Leg	muscle
3	chr3:134071000-134088800	Enhancers	Right Atrium	heart
4	chr3:134072200-134090200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:134072400-134091200	Genic enhancers	Spleen	Spleen
6	chr3:134072800-134090600	Genic enhancers	Left Ventricle	heart
7	chr3:134073000-134089400	Genic enhancers	HMEC	breast
8	chr3:134073400-134091400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:134074400-134089400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:134075000-134090400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:134076800-134088600	Genic enhancers	NHDF-Ad	bronchial
12	chr3:134078800-134090400	Genic enhancers	Liver	Liver
13	chr3:134079400-134089600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:134081400-134090600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:134081600-134091000	Enhancers	Psoas Muscle	Psoas
16	chr3:134082000-134089800	Genic enhancers	Placenta Amnion	Placenta Amnion
17	chr3:134082000-134090800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:134082000-134090800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:134082000-134091000	Genic enhancers	Fetal Stomach	stomach
20	chr3:134082200-134090200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:134082200-134092800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:134082400-134091400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:134083000-134088600	Genic enhancers	NHLF	lung
24	chr3:134083000-134089400	Genic enhancers	Colon Smooth Muscle	Colon
25	chr3:134083200-134089600	Genic enhancers	Placenta	Placenta
26	chr3:134083400-134089200	Genic enhancers	NHEK	skin
27	chr3:134083600-134089000	Genic enhancers	HSMMtube	muscle
28	chr3:134083600-134089800	Genic enhancers	Brain Angular Gyrus	brain
29	chr3:134083600-134090000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr3:134083600-134090800	Genic enhancers	Fetal Intestine Large	intestine
31	chr3:134083800-134088800	Genic enhancers	Brain Inferior Temporal Lobe	brain
32	chr3:134083800-134090000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
33	chr3:134084000-134089000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:134084000-134090000	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:134084000-134090200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:134084000-134090200	Genic enhancers	Duodenum Mucosa	Duodenum
37	chr3:134084000-134090800	Genic enhancers	Lung	lung
38	chr3:134084200-134089200	Genic enhancers	Brain Anterior Caudate	brain
39	chr3:134084200-134089400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
40	chr3:134084200-134090000	Genic enhancers	Brain Germinal Matrix	brain
41	chr3:134084400-134088800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:134084400-134088800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:134084400-134089400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
44	chr3:134084600-134089400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:134084600-134089600	Weak transcription	Fetal Thymus	thymus
46	chr3:134084600-134090000	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr3:134084600-134090400	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr3:134084600-134090800	Genic enhancers	Aorta	Aorta
49	chr3:134084800-134088800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:134084800-134089200	Weak transcription	Small Intestine	intestine

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