Variant report

Variant	rs8030014
Chromosome Location	chr15:75640569-75640570
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	POLR2A	chr15:75640473-75641030	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr15:75640514-75641584	A549	lung:	n/a	chr15:75640729-75640749
3	BCL3	chr15:75639663-75643792	A549	lung:	n/a	chr15:75640106-75640115 chr15:75640555-75640568 chr15:75640920-75640933 chr15:75641197-75641210 chr15:75641104-75641117 chr15:75640631-75640644 chr15:75640116-75640129 chr15:75640402-75640415 chr15:75640553-75640566
4	MAZ	chr15:75639547-75640860	K562	blood:	n/a	chr15:75640504-75640513 chr15:75640284-75640294
5	EGR1	chr15:75640316-75640755	K562	blood:	n/a	chr15:75640518-75640528 chr15:75640712-75640725
6	YY1	chr15:75640376-75640639	GM12891	blood:	n/a	chr15:75640559-75640568 chr15:75640557-75640568
7	POLR2A	chr15:75639801-75641869	Hela-S3	cervix:	n/a	n/a
8	MTA3	chr15:75639058-75641874	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:75640396-75640569	GM12878	blood:	n/a	n/a
10	TEAD4	chr15:75639568-75640737	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr15:75639357-75640583	GM12891	blood:	n/a	n/a
12	ZBTB7A	chr15:75639482-75641031	ECC-1	luminal epithelium:	n/a	chr15:75640067-75640081 chr15:75640074-75640082 chr15:75640280-75640289
13	POLR2A	chr15:75638898-75643996	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr15:75640512-75640788	HCT-116	colon:	n/a	n/a
15	MAZ	chr15:75640556-75640723	HepG2	liver:	n/a	n/a
16	POLR2A	chr15:75639405-75643959	A549	lung:	n/a	n/a
17	HMGN3	chr15:75639489-75640627	K562	blood:	n/a	n/a
18	TAF1	chr15:75639696-75640676	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr15:75640409-75641837	A549	lung:	n/a	n/a
20	CREB1	chr15:75639749-75640571	A549	lung:	n/a	n/a
21	CCNT2	chr15:75640362-75640719	K562	blood:	n/a	chr15:75640384-75640393 chr15:75640710-75640719
22	MAX	chr15:75639535-75640819	ECC-1	luminal epithelium:	n/a	chr15:75640504-75640513 chr15:75640284-75640294
23	ELF1	chr15:75640373-75640658	K562	blood:	n/a	chr15:75640403-75640412
24	POLR2A	chr15:75640176-75643267	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr15:75640397-75640602	MCF-7	breast:	n/a	n/a
26	HCFC1	chr15:75639020-75642782	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr15:75640471-75641873	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr15:75639514-75641760	MCF10A-Er-Src	breast:	n/a	n/a
29	YY1	chr15:75640327-75640685	ECC-1	luminal epithelium:	n/a	chr15:75640559-75640568 chr15:75640557-75640568
30	MAX	chr15:75639620-75641358	A549	lung:	n/a	chr15:75640504-75640513 chr15:75640284-75640294
31	ZBTB7A	chr15:75640472-75640907	K562	blood:	n/a	n/a
32	MAZ	chr15:75639431-75641430	IMR90	lung:	n/a	chr15:75640504-75640513 chr15:75640284-75640294
33	JUND	chr15:75640109-75642004	A549	lung:	n/a	chr15:75640519-75640528
34	YY1	chr15:75640348-75640638	K562	blood:	n/a	chr15:75640559-75640568 chr15:75640557-75640568
35	UBTF	chr15:75640287-75641016	K562	blood:	n/a	n/a
36	POLR2A	chr15:75640338-75640758	HUVEC	blood vessel:	n/a	n/a
37	EGR1	chr15:75640371-75640733	K562	blood:	n/a	chr15:75640518-75640528 chr15:75640712-75640725
38	POLR2A	chr15:75640194-75640725	HUVEC	blood vessel:	n/a	n/a
39	ZBTB7A	chr15:75639488-75641125	ECC-1	luminal epithelium:	n/a	chr15:75640067-75640081 chr15:75640074-75640082 chr15:75640280-75640289
40	POLR2A	chr15:75640332-75640894	K562	blood:	n/a	n/a
41	POLR2A	chr15:75639147-75642318	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr15:75639188-75643769	Hela-S3	cervix:	n/a	n/a
43	PBX3	chr15:75639576-75641891	SK-N-SH	brain:	n/a	chr15:75640729-75640749
44	SMARCB1	chr15:75639580-75641716	Hela-S3	cervix:	n/a	chr15:75639902-75639911
45	BCL3	chr15:75639824-75641937	A549	lung:	n/a	chr15:75640106-75640115 chr15:75640555-75640568 chr15:75640920-75640933 chr15:75641197-75641210 chr15:75641104-75641117 chr15:75640631-75640644 chr15:75640116-75640129 chr15:75640402-75640415 chr15:75640553-75640566
46	TCF12	chr15:75640374-75640954	ECC-1	luminal epithelium:	n/a	chr15:75640857-75640867
47	POLR2A	chr15:75639407-75641966	ECC-1	luminal epithelium:	n/a	n/a
48	SIN3A	chr15:75639233-75641378	H1-hESC	embryonic stem cell:	n/a	chr15:75640225-75640238 chr15:75640398-75640407 chr15:75640487-75640500 chr15:75640401-75640414
49	YY1	chr15:75639499-75640824	HepG2	liver:	n/a	chr15:75640710-75640721 chr15:75640559-75640568 chr15:75640557-75640568
50	UBTF	chr15:75640487-75640846	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75639207..75640858-chr15:75743116..75744779,2	MCF-7	breast:
2	chr15:75626494..75629832-chr15:75639090..75642248,3	MCF-7	breast:

Variant related genes	Relation type
NEIL1	TF binding region
ENSG00000169375	Chromatin interaction
ENSG00000140365	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11072544	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1128933	0.91[EUR][1000 genomes]
rs11853141	0.82[ASN][1000 genomes]
rs12915221	0.90[EUR][1000 genomes]
rs3809549	0.91[EUR][1000 genomes]
rs4462560	0.83[ASN][1000 genomes]
rs4526985	0.88[EUR][1000 genomes]
rs4886442	0.88[EUR][1000 genomes]
rs4886702	0.85[EUR][1000 genomes]
rs4886704	0.86[EUR][1000 genomes]
rs6495172	0.90[EUR][1000 genomes]
rs6495173	0.89[EUR][1000 genomes]
rs6495174	0.90[EUR][1000 genomes]
rs6495176	0.86[EUR][1000 genomes]
rs7163783	0.86[EUR][1000 genomes]
rs7165292	0.88[EUR][1000 genomes]
rs7165469	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7170660	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7173220	0.89[EUR][1000 genomes]
rs7175139	0.86[EUR][1000 genomes]
rs7182283	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv482859	chr15:75493899-75688451	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv1035829	chr15:75504534-75692417	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
6	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
8	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
9	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8030014	MAN2C1	cis	Whole Blood	GTEx
rs8030014	MAN2C1	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75633600-75641000	Weak transcription	Dnd41	blood
2	chr15:75638800-75640800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr15:75638800-75641200	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr15:75639000-75640800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr15:75639000-75640800	Active TSS	Brain Substantia Nigra	brain
6	chr15:75639000-75640800	Active TSS	Colonic Mucosa	Colon
7	chr15:75639000-75640800	Active TSS	Fetal Brain Female	brain
8	chr15:75639000-75640800	Active TSS	Thymus	Thymus
9	chr15:75639000-75641000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr15:75639000-75641000	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr15:75639000-75641000	Active TSS	Brain Anterior Caudate	brain
12	chr15:75639000-75641000	Active TSS	Colon Smooth Muscle	Colon
13	chr15:75639000-75641000	Active TSS	Rectal Smooth Muscle	rectum
14	chr15:75639000-75641000	Active TSS	Right Atrium	heart
15	chr15:75639000-75641200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr15:75639000-75641400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:75639000-75641400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr15:75639000-75641400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:75639000-75641600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr15:75639000-75641600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr15:75639000-75641600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr15:75639200-75640600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:75639200-75640800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:75639200-75640800	Active TSS	Brain Cingulate Gyrus	brain
25	chr15:75639200-75640800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:75639200-75640800	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr15:75639200-75640800	Active TSS	Esophagus	oesophagus
28	chr15:75639200-75640800	Bivalent/Poised TSS	Fetal Lung	lung
29	chr15:75639200-75640800	Active TSS	Gastric	stomach
30	chr15:75639200-75640800	Active TSS	Ovary	ovary
31	chr15:75639200-75640800	Active TSS	Placenta Amnion	Placenta Amnion
32	chr15:75639200-75641000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr15:75639200-75641000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chr15:75639200-75641000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:75639200-75641000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
36	chr15:75639200-75641000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr15:75639200-75641000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr15:75639200-75641000	Active TSS	Aorta	Aorta
39	chr15:75639200-75641000	Active TSS	Fetal Intestine Large	intestine
40	chr15:75639200-75641000	Active TSS	Fetal Intestine Small	intestine
41	chr15:75639200-75641000	Flanking Active TSS	Placenta	Placenta
42	chr15:75639200-75641000	Active TSS	Small Intestine	intestine
43	chr15:75639200-75641200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:75639200-75641200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
45	chr15:75639200-75641200	Active TSS	Fetal Kidney	kidney
46	chr15:75639200-75641200	Active TSS	Psoas Muscle	Psoas
47	chr15:75639200-75641400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
48	chr15:75639200-75641400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
49	chr15:75639200-75641400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
50	chr15:75639400-75640600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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