Variant report

Variant	rs73398512
Chromosome Location	chr15:41059290-41059291
allele	C/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	CTCF	chr15:41059160-41059310	HCPEpiC	choroid plexus:	n/a	n/a
2	POLR2A	chr15:41058900-41059310	K562	blood:	n/a	n/a
3	POLR2A	chr15:41055349-41059478	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr15:41057635-41061953	K562	blood:	n/a	n/a
5	POLR2A	chr15:41057608-41059993	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr15:41059215-41059698	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:41059282-41059803	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:41059203-41059636	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:41059112-41059491	SK-N-SH	brain:	n/a	n/a
10	JUND	chr15:41059234-41059434	H1-hESC	embryonic stem cell:	n/a	chr15:41059318-41059328 chr15:41059318-41059328 chr15:41059315-41059326
11	JUND	chr15:41059235-41059353	H1-hESC	embryonic stem cell:	n/a	chr15:41059318-41059328 chr15:41059318-41059328 chr15:41059315-41059326
12	POLR2A	chr15:41055973-41059813	K562	blood:	n/a	n/a
13	FOS	chr15:41059159-41059451	MCF10A-Er-Src	breast:	n/a	chr15:41059318-41059328 chr15:41059318-41059328 chr15:41059315-41059326
14	RCOR1	chr15:41059267-41059319	Hela-S3	cervix:	n/a	n/a
15	FOS	chr15:41059166-41059493	MCF10A-Er-Src	breast:	n/a	chr15:41059318-41059328 chr15:41059318-41059328 chr15:41059315-41059326
16	POLR2A	chr15:41059154-41059523	GM12892	blood:	n/a	n/a
17	POLR2A	chr15:41059159-41059736	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr15:41059244-41059622	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:41057591-41062786	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr15:41059163-41059661	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr15:41059200-41059350	HEEpiC	esophagus:	n/a	n/a
22	FOS	chr15:41059165-41059451	MCF10A-Er-Src	breast:	n/a	chr15:41059318-41059328 chr15:41059318-41059328 chr15:41059315-41059326
23	POLR2A	chr15:41059117-41059953	GM12892	blood:	n/a	n/a
24	POLR2A	chr15:41059074-41061819	K562	blood:	n/a	n/a
25	MYC	chr15:41058934-41059383	MCF10A-Er-Src	breast:	n/a	chr15:41059269-41059279
26	CTCF	chr15:41059200-41059350	AG04449	skin:	n/a	n/a
27	POLR2A	chr15:41059186-41059661	HepG2	liver:	n/a	n/a
28	MYC	chr15:41059242-41059373	MCF10A-Er-Src	breast:	n/a	chr15:41059269-41059279
29	STAT3	chr15:41058922-41059348	MCF10A-Er-Src	breast:	n/a	chr15:41059219-41059230
30	POLR2A	chr15:41059033-41059620	Hela-S3	cervix:	n/a	n/a
31	JUND	chr15:41058981-41059660	SK-N-SH	brain:	n/a	chr15:41059318-41059328 chr15:41059318-41059328 chr15:41059315-41059326
32	MAZ	chr15:41059251-41059437	Hela-S3	cervix:	n/a	chr15:41059269-41059279
33	FOSL2	chr15:41059138-41059729	SK-N-SH	brain:	n/a	chr15:41059318-41059328 chr15:41059318-41059328 chr15:41059315-41059326
34	HCFC1	chr15:41054658-41062813	Hela-S3	cervix:	n/a	n/a
35	FOS	chr15:41059202-41059448	MCF10A-Er-Src	breast:	n/a	chr15:41059318-41059328 chr15:41059318-41059328 chr15:41059315-41059326
36	POLR2A	chr15:41059244-41059313	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr15:41059083-41060095	HepG2	liver:	n/a	n/a
38	POLR2A	chr15:41059180-41059534	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr15:41059107-41059839	GM12878	blood:	n/a	n/a
40	STAT3	chr15:41059191-41059350	MCF10A-Er-Src	breast:	n/a	chr15:41059219-41059230

No.	Distal block	Cell Line	Cell type
1	chr15:41058869..41059639-chr21:38444005..38444923,2	Hela-S3	cervix:
2	chr15:41042059..41049706-chr15:41053861..41061949,15	MCF-7	breast:
3	chr15:41059265..41060152-chr5:168006202..168006986,2	Hela-S3	cervix:
4	chr15:41058103..41060724-chr15:41061996..41063790,2	MCF-7	breast:
5	chr15:41047666..41050190-chr15:41058981..41061979,2	MCF-7	breast:
6	chr15:41053928..41056375-chr15:41057436..41059478,2	MCF-7	breast:
7	chr15:41054628..41058503-chr15:41058814..41065530,15	K562	blood:
8	chr15:41055716..41060288-chr15:41072655..41077591,4	MCF-7	breast:

Variant related genes	Relation type
C15orf62	TF binding region
ENSG00000104129	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000185808	Chromatin interaction
ENSG00000188277	Chromatin interaction
ENSG00000120137	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11070287	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12050702	0.84[ASN][1000 genomes]
rs12102251	0.85[AMR][1000 genomes]
rs16970995	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16970997	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16971004	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16971008	0.83[AMR][1000 genomes]
rs16971013	1.00[AMR][1000 genomes]
rs16971015	1.00[AMR][1000 genomes]
rs1814415	0.85[AMR][1000 genomes]
rs2004043	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2412552	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28460049	0.85[AMR][1000 genomes]
rs28480346	1.00[AMR][1000 genomes]
rs28498351	1.00[AMR][1000 genomes]
rs28578011	0.85[AMR][1000 genomes]
rs28716513	0.83[AMR][1000 genomes]
rs28718778	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28727420	0.85[AMR][1000 genomes]
rs28736321	0.85[AMR][1000 genomes]
rs34819163	0.83[AMR][1000 genomes]
rs4343248	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56390641	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57191378	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57380807	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58036350	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61317135	1.00[AMR][1000 genomes]
rs61405952	0.85[AMR][1000 genomes]
rs6492966	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7165694	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166719	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7172251	0.83[AMR][1000 genomes]
rs7177590	0.84[ASN][1000 genomes]
rs7178363	0.85[AMR][1000 genomes]
rs7180036	0.89[ASN][1000 genomes]
rs7182456	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73398510	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73398517	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398522	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398528	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398537	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398540	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398560	0.85[AMR][1000 genomes]
rs73398591	0.85[AMR][1000 genomes]
rs8042758	0.88[ASN][1000 genomes]
rs934783	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41056800-41059400	Weak transcription	Brain Anterior Caudate	brain
2	chr15:41057000-41059400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:41057000-41059400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:41057000-41059400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr15:41057000-41059800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr15:41057000-41060000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr15:41057000-41060200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:41057000-41062200	Weak transcription	Aorta	Aorta
9	chr15:41057000-41062600	Enhancers	NH-A	brain
10	chr15:41057200-41059400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:41057200-41059400	Weak transcription	Right Ventricle	heart
12	chr15:41057200-41059400	Enhancers	NHLF	lung
13	chr15:41057200-41059800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr15:41057200-41059800	Weak transcription	Brain Substantia Nigra	brain
15	chr15:41057200-41060000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr15:41057200-41061200	Weak transcription	Right Atrium	heart
17	chr15:41057200-41063200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:41057200-41063400	Weak transcription	HSMMtube	muscle
19	chr15:41057200-41063800	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:41057200-41065400	Weak transcription	Brain Angular Gyrus	brain
21	chr15:41057200-41068200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr15:41057400-41059600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:41057400-41059600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:41057400-41061200	Weak transcription	Fetal Brain Male	brain
25	chr15:41057400-41063200	Enhancers	Stomach Mucosa	stomach
26	chr15:41057400-41070800	Weak transcription	Psoas Muscle	Psoas
27	chr15:41057600-41059600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr15:41057600-41059600	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr15:41057600-41059800	Genic enhancers	Liver	Liver
30	chr15:41057600-41060000	Weak transcription	Small Intestine	intestine
31	chr15:41057600-41062600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr15:41057600-41063800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:41057600-41066600	Weak transcription	Fetal Heart	heart
34	chr15:41057600-41067400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:41057800-41059800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:41057800-41060800	Weak transcription	Primary T cells from cord blood	blood
37	chr15:41057800-41063200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:41058000-41059400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:41058000-41059400	Weak transcription	HUVEC	blood vessel
40	chr15:41058000-41059400	Enhancers	K562	blood
41	chr15:41058000-41059800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:41058000-41060200	Weak transcription	Primary B cells from cord blood	blood
43	chr15:41058000-41060600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr15:41058000-41060800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr15:41058000-41060800	Transcr. at gene 5' and 3'	Hela-S3	cervix
46	chr15:41058000-41061200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr15:41058000-41063400	Weak transcription	Left Ventricle	heart
48	chr15:41058000-41069000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr15:41058200-41059400	Weak transcription	Ovary	ovary
50	chr15:41058200-41059600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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