Variant report

Variant	rs12492644
Chromosome Location	chr3:194984250-194984251
allele	A/G
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	TEAD4	chr3:194983775-194984354	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:194978258..194982064-chr3:194982349..194986625,5	MCF-7	breast:
2	chr3:194390925..194393722-chr3:194982636..194985275,2	MCF-7	breast:
3	chr3:194961621..194965085-chr3:194983168..194985887,3	K562	blood:
4	chr3:194979343..194985907-chr3:194989595..194992143,7	K562	blood:

Variant related genes	Relation type
XXYLT1	TF binding region
ENSG00000173950	Chromatin interaction
ENSG00000041802	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10933702	0.95[EUR][1000 genomes]
rs10933703	0.95[EUR][1000 genomes]
rs11917438	0.95[EUR][1000 genomes]
rs11919965	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11921174	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11928199	0.92[ASN][1000 genomes]
rs12485302	0.83[AMR][1000 genomes]
rs12485800	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12486168	0.95[EUR][1000 genomes]
rs12486220	0.95[EUR][1000 genomes]
rs12486805	0.80[AMR][1000 genomes]
rs12486835	0.95[EUR][1000 genomes]
rs12488451	0.80[AMR][1000 genomes]
rs12488481	0.80[AMR][1000 genomes]
rs12488616	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12488979	0.80[AMR][1000 genomes]
rs12489090	0.80[AMR][1000 genomes]
rs12489849	0.80[AMR][1000 genomes]
rs12490658	0.80[AMR][1000 genomes]
rs12491026	0.80[AMR][1000 genomes]
rs12491371	0.80[AMR][1000 genomes]
rs12491426	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12491670	0.80[AMR][1000 genomes]
rs12491736	0.80[AMR][1000 genomes]
rs12491902	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12492289	0.85[EUR][1000 genomes]
rs12492552	0.80[AMR][1000 genomes]
rs12493888	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494306	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12494759	0.80[AMR][1000 genomes]
rs12494773	0.80[AMR][1000 genomes]
rs12495657	0.80[AMR][1000 genomes]
rs12495659	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12496204	0.80[AMR][1000 genomes]
rs12496628	0.90[EUR][1000 genomes]
rs12497478	0.80[AMR][1000 genomes]
rs12497906	0.92[ASN][1000 genomes]
rs12498063	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1808074	0.83[AMR][1000 genomes]
rs2050807	0.80[AMR][1000 genomes]
rs2050808	0.80[AMR][1000 genomes]
rs34643420	0.80[AMR][1000 genomes]
rs35899174	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3773419	0.83[AMR][1000 genomes]
rs3773420	0.83[AMR][1000 genomes]
rs41266999	0.80[AMR][1000 genomes]
rs41267003	0.80[AMR][1000 genomes]
rs56835677	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58113840	0.84[EUR][1000 genomes]
rs59579668	0.95[EUR][1000 genomes]
rs61022222	0.84[EUR][1000 genomes]
rs6437466	0.95[EUR][1000 genomes]
rs66510151	0.84[EUR][1000 genomes]
rs67388686	0.95[EUR][1000 genomes]
rs67484513	0.84[EUR][1000 genomes]
rs6777904	0.84[EUR][1000 genomes]
rs6785108	0.90[EUR][1000 genomes]
rs6790425	0.91[ASN][1000 genomes]
rs6804467	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72499624	0.84[EUR][1000 genomes]
rs72607893	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72607894	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72607895	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72607896	0.83[AMR][1000 genomes]
rs72607897	0.83[AMR][1000 genomes]
rs72607898	0.83[AMR][1000 genomes]
rs72607899	0.83[AMR][1000 genomes]
rs72607900	0.83[AMR][1000 genomes]
rs72607901	0.83[AMR][1000 genomes]
rs72607902	0.83[AMR][1000 genomes]
rs72611103	0.83[AMR][1000 genomes]
rs755202	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7642127	0.90[EUR][1000 genomes]
rs999331	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
6	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
7	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
12	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
13	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
14	nsv984539	chr3:194945800-194984579	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
15	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194981400-194984400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:194981400-194987800	Weak transcription	Psoas Muscle	Psoas
3	chr3:194981400-194990000	Weak transcription	HSMMtube	muscle
4	chr3:194981400-194990800	Weak transcription	Aorta	Aorta
5	chr3:194981600-194984800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:194981600-194984800	Weak transcription	HMEC	breast
7	chr3:194981600-194985000	Weak transcription	K562	blood
8	chr3:194981600-194986000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:194981600-194986200	Weak transcription	Hela-S3	cervix
10	chr3:194981600-194986400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:194981600-194986400	Weak transcription	Left Ventricle	heart
12	chr3:194981600-194986400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:194981600-194986800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:194981600-194987000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:194981600-194989600	Weak transcription	Right Ventricle	heart
16	chr3:194981600-194989800	Weak transcription	Brain Substantia Nigra	brain
17	chr3:194981600-194990000	Weak transcription	A549	lung
18	chr3:194981600-194990200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:194981600-194990200	Weak transcription	HSMM	muscle
20	chr3:194981600-194990600	Weak transcription	Ovary	ovary
21	chr3:194981800-194984600	Weak transcription	Esophagus	oesophagus
22	chr3:194981800-194984800	Weak transcription	Fetal Stomach	stomach
23	chr3:194981800-194986000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:194981800-194986200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:194981800-194986200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:194981800-194986200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:194981800-194986200	Weak transcription	NHLF	lung
28	chr3:194981800-194986400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:194981800-194986600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:194981800-194986600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:194981800-194986800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:194981800-194987200	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:194981800-194987400	Weak transcription	Brain Germinal Matrix	brain
34	chr3:194981800-194987800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:194981800-194987800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:194981800-194987800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:194981800-194989400	Weak transcription	Brain Angular Gyrus	brain
38	chr3:194981800-194989400	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:194981800-194989400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:194981800-194989600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:194981800-194989600	Weak transcription	Liver	Liver
42	chr3:194981800-194989600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:194981800-194989600	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:194981800-194989600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:194981800-194989600	Weak transcription	Fetal Heart	heart
46	chr3:194981800-194989600	Weak transcription	Lung	lung
47	chr3:194981800-194989600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:194981800-194989800	Weak transcription	Adipose Nuclei	Adipose
49	chr3:194981800-194989800	Weak transcription	Colonic Mucosa	Colon
50	chr3:194981800-194989800	Weak transcription	Fetal Brain Female	brain

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