Variant report

Variant	rs17073188
Chromosome Location	chr13:50144197-50144198
allele	G/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	STAT3	chr13:50143913-50144562	MCF10A-Er-Src	breast:	n/a	chr13:50144198-50144212 chr13:50144201-50144210 chr13:50144200-50144209
2	GATA3	chr13:50144009-50144722	MCF-7	breast:	n/a	n/a
3	JUND	chr13:50144100-50144456	Hela-S3	cervix:	n/a	chr13:50144279-50144287 chr13:50144276-50144285 chr13:50144276-50144283 chr13:50144274-50144285
4	JUND	chr13:50144141-50144459	HepG2	liver:	n/a	chr13:50144279-50144287 chr13:50144276-50144285 chr13:50144276-50144283 chr13:50144274-50144285
5	EP300	chr13:50144171-50144445	Hela-S3	cervix:	n/a	chr13:50144295-50144303 chr13:50144253-50144260 chr13:50144276-50144285
6	FOS	chr13:50144165-50144433	HUVEC	blood vessel:	n/a	chr13:50144279-50144287 chr13:50144276-50144285 chr13:50144274-50144285 chr13:50144276-50144283
7	STAT3	chr13:50144170-50144431	MCF10A-Er-Src	breast:	n/a	chr13:50144198-50144212 chr13:50144201-50144210 chr13:50144200-50144209
8	SIN3AK20	chr13:50143969-50144725	MCF-7	breast:	n/a	n/a
9	RUNX3	chr13:50144136-50144900	GM12878	blood:	n/a	n/a
10	FOS	chr13:50144062-50144552	MCF10A-Er-Src	breast:	n/a	chr13:50144279-50144287 chr13:50144276-50144285 chr13:50144274-50144285 chr13:50144276-50144283
11	CEBPB	chr13:50143875-50144532	MCF-7	breast:	n/a	chr13:50144394-50144411
12	GATA3	chr13:50143858-50144759	MCF-7	breast:	n/a	n/a
13	RELA	chr13:50144181-50144921	GM12878	blood:	n/a	n/a
14	MYC	chr13:50144152-50144559	MCF10A-Er-Src	breast:	n/a	n/a
15	NR2F2	chr13:50143764-50144650	MCF-7	breast:	n/a	n/a
16	STAT3	chr13:50144126-50144419	Hela-S3	cervix:	n/a	chr13:50144198-50144212 chr13:50144201-50144210 chr13:50144200-50144209
17	CEBPB	chr13:50144145-50144564	Hela-S3	cervix:	n/a	chr13:50144394-50144411
18	JUND	chr13:50144096-50144580	MCF-7	breast:	n/a	chr13:50144279-50144287 chr13:50144276-50144285 chr13:50144276-50144283 chr13:50144274-50144285
19	STAT3	chr13:50144010-50144725	MCF10A-Er-Src	breast:	n/a	chr13:50144198-50144212 chr13:50144201-50144210 chr13:50144200-50144209
20	FOS	chr13:50144033-50144622	MCF10A-Er-Src	breast:	n/a	chr13:50144279-50144287 chr13:50144276-50144285 chr13:50144274-50144285 chr13:50144276-50144283
21	STAT3	chr13:50144017-50144652	MCF10A-Er-Src	breast:	n/a	chr13:50144198-50144212 chr13:50144201-50144210 chr13:50144200-50144209
22	FOS	chr13:50144092-50144555	MCF10A-Er-Src	breast:	n/a	chr13:50144279-50144287 chr13:50144276-50144285 chr13:50144274-50144285 chr13:50144276-50144283
23	FOSL2	chr13:50144067-50144559	MCF-7	breast:	n/a	chr13:50144279-50144287 chr13:50144276-50144285 chr13:50144276-50144283
24	ZNF217	chr13:50144090-50144525	MCF-7	breast:	n/a	n/a
25	JUND	chr13:50143969-50144681	SK-N-SH	brain:	n/a	chr13:50144279-50144287 chr13:50144276-50144285 chr13:50144276-50144283 chr13:50144274-50144285
26	FOS	chr13:50144036-50144562	MCF10A-Er-Src	breast:	n/a	chr13:50144279-50144287 chr13:50144276-50144285 chr13:50144274-50144285 chr13:50144276-50144283
27	MYC	chr13:50144170-50144502	MCF10A-Er-Src	breast:	n/a	n/a
28	E2F4	chr13:50144117-50144434	MCF10A-Er-Src	breast:	n/a	n/a
29	CEBPB	chr13:50144187-50144589	MCF-7	breast:	n/a	chr13:50144394-50144411

No.	Distal block	Cell Line	Cell type
1	chr13:50134986..50135758-chr13:50143919..50144828,2	MCF-7	breast:
2	chr13:50068857..50071479-chr13:50143285..50145487,2	MCF-7	breast:
3	chr13:50142756..50146527-chr13:50158016..50161593,4	MCF-7	breast:
4	chr13:50038641..50040451-chr13:50143314..50145864,2	MCF-7	breast:
5	chr13:50143262..50147042-chr13:50150087..50153613,4	MCF-7	breast:
6	chr13:50016440..50019751-chr13:50141127..50144444,4	MCF-7	breast:
7	chr13:50134505..50135459-chr13:50143778..50144515,3	MCF-7	breast:
8	chr13:50143614..50146624-chr13:50158019..50161696,4	MCF-7	breast:

Variant related genes	Relation type
RCBTB1	TF binding region
ENSG00000136147	Chromatin interaction
ENSG00000102547	Chromatin interaction
ENSG00000136144	Chromatin interaction
ENSG00000136169	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12583474	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12585829	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1325658	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1325659	0.90[JPT][hapmap]
rs1830628	0.90[ASN][1000 genomes]
rs1985597	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4941651	0.90[ASN][1000 genomes]
rs62637574	0.88[AFR][1000 genomes]
rs7331327	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7336812	0.85[JPT][hapmap]
rs7982423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316467	0.85[JPT][hapmap]
rs9743423	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv1052801	chr13:50116407-50144995	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv561616	chr13:50120435-50190246	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv1046912	chr13:50122840-50189313	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv1043902	chr13:50122840-50189999	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	esv2761789	chr13:50122852-50185910	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	nsv455883	chr13:50124621-50185204	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv561617	chr13:50124621-50185204	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
17	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50088400-50151000	Weak transcription	Psoas Muscle	Psoas
2	chr13:50108600-50158800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:50122000-50158000	Weak transcription	Brain Germinal Matrix	brain
4	chr13:50124000-50158800	Weak transcription	Esophagus	oesophagus
5	chr13:50126400-50152400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr13:50129000-50158800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:50129800-50155200	Weak transcription	Spleen	Spleen
8	chr13:50130000-50144200	Weak transcription	GM12878-XiMat	blood
9	chr13:50130400-50158800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr13:50132400-50153600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr13:50132400-50153800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr13:50132400-50153800	Weak transcription	NH-A	brain
13	chr13:50133400-50154000	Weak transcription	Colon Smooth Muscle	Colon
14	chr13:50134200-50151000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr13:50134200-50158400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr13:50134200-50158400	Weak transcription	Fetal Brain Female	brain
17	chr13:50134400-50151000	Weak transcription	HSMMtube	muscle
18	chr13:50135000-50158600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr13:50135200-50144200	Weak transcription	A549	lung
20	chr13:50135200-50144400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr13:50135200-50153400	Weak transcription	Gastric	stomach
22	chr13:50135200-50154000	Weak transcription	Placenta	Placenta
23	chr13:50135400-50145600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr13:50135600-50144200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr13:50135600-50151000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr13:50135600-50151200	Weak transcription	Aorta	Aorta
27	chr13:50135600-50153800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr13:50135600-50155200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr13:50135600-50158000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr13:50135600-50158400	Weak transcription	Osteobl	bone
31	chr13:50135800-50153600	Weak transcription	HepG2	liver
32	chr13:50136200-50152200	Weak transcription	Primary B cells from cord blood	blood
33	chr13:50138200-50153400	Weak transcription	Thymus	Thymus
34	chr13:50138400-50153800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr13:50138600-50152200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr13:50138600-50157200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr13:50138800-50146200	Weak transcription	Fetal Stomach	stomach
38	chr13:50139200-50153000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr13:50139200-50153000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr13:50139200-50153200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr13:50139400-50153400	Weak transcription	Fetal Intestine Small	intestine
42	chr13:50139400-50153600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr13:50139400-50159000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr13:50139600-50153400	Weak transcription	Lung	lung
45	chr13:50140800-50153800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr13:50140800-50154200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr13:50140800-50158000	Weak transcription	Fetal Brain Male	brain
48	chr13:50141000-50153200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr13:50141000-50153800	Weak transcription	Adipose Nuclei	Adipose
50	chr13:50141000-50153800	Weak transcription	Liver	Liver

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