Variant report

Variant	rs11634109
Chromosome Location	chr15:75643714-75643715
allele	C/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	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
2	POLR2A	chr15:75641986-75643786	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr15:75641982-75644137	K562	blood:	n/a	n/a
4	POLR2A	chr15:75642220-75643888	GM12892	blood:	n/a	n/a
5	POLR2A	chr15:75638898-75643996	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr15:75639405-75643959	A549	lung:	n/a	n/a
7	POLR2A	chr15:75642187-75643790	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr15:75641880-75643807	GM12892	blood:	n/a	n/a
9	POLR2A	chr15:75642027-75643757	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr15:75642193-75643771	PBDE	blood:	n/a	n/a
11	POLR2A	chr15:75642029-75643822	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr15:75642022-75643826	GM12891	blood:	n/a	n/a
13	POLR2A	chr15:75641993-75643896	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr15:75643239-75643827	HCT-116	colon:	n/a	n/a
15	POLR2A	chr15:75642164-75643940	GM12892	blood:	n/a	n/a
16	POLR2A	chr15:75641993-75643997	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr15:75639188-75643769	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr15:75642041-75643952	K562	blood:	n/a	n/a
19	POLR2A	chr15:75642074-75643776	GM12892	blood:	n/a	n/a
20	POLR2A	chr15:75642113-75643948	HepG2	liver:	n/a	n/a
21	POLR2A	chr15:75639141-75646939	HepG2	liver:	n/a	n/a
22	POLR2A	chr15:75642063-75644042	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr15:75639250-75643938	K562	blood:	n/a	n/a
24	POLR2A	chr15:75639819-75643955	K562	blood:	n/a	n/a
25	POLR2A	chr15:75642948-75643731	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr15:75642055-75643772	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75626956..75629637-chr15:75642872..75644867,2	MCF-7	breast:

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

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1809714	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1984586	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1984587	0.89[EUR][1000 genomes]
rs3866545	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4310817	0.90[EUR][1000 genomes]
rs4886684	0.83[EUR][1000 genomes]
rs55653892	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56164452	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59084522	0.87[EUR][1000 genomes]
rs7164167	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7164429	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7166436	0.90[EUR][1000 genomes]
rs7166852	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7167401	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7183520	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73435015	0.87[EUR][1000 genomes]
rs73435089	0.87[EUR][1000 genomes]
rs73436803	0.90[EUR][1000 genomes]
rs73436854	0.84[EUR][1000 genomes]
rs8027749	0.81[EUR][1000 genomes]
rs8031650	0.86[EUR][1000 genomes]
rs9673084	0.83[AMR][1000 genomes];0.90[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11634109	MAN2C1	cis	Whole Blood	GTEx
rs11634109	CTD-2323K18.1	cis	Thyroid	GTEx
rs11634109	MAN2C1	cis	Esophagus Muscularis	GTEx
rs11634109	SNUPN	cis	Thyroid	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75641000-75645200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
2	chr15:75641200-75644800	Weak transcription	A549	lung
3	chr15:75641200-75646800	Weak transcription	Aorta	Aorta
4	chr15:75641200-75655000	Weak transcription	K562	blood
5	chr15:75641400-75645600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:75641400-75646800	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:75641400-75646800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:75641400-75647200	Weak transcription	Brain Anterior Caudate	brain
9	chr15:75641400-75647400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:75641400-75647400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr15:75641400-75647800	Weak transcription	Ovary	ovary
12	chr15:75641400-75648200	Weak transcription	Psoas Muscle	Psoas
13	chr15:75641400-75651200	Weak transcription	HSMM	muscle
14	chr15:75641400-75655400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:75641400-75658600	Weak transcription	HUVEC	blood vessel
16	chr15:75641600-75644400	Weak transcription	Liver	Liver
17	chr15:75641600-75644600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:75641600-75645800	Weak transcription	HepG2	liver
19	chr15:75641600-75647000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:75641600-75647200	Weak transcription	Brain Angular Gyrus	brain
21	chr15:75641600-75647200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:75641600-75647400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr15:75641600-75647400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:75641600-75647800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:75641600-75648200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:75641600-75648400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:75641600-75648400	Weak transcription	Colon Smooth Muscle	Colon
28	chr15:75641600-75648400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr15:75641600-75648800	Weak transcription	Fetal Lung	lung
30	chr15:75641600-75650400	Weak transcription	Brain Substantia Nigra	brain
31	chr15:75641600-75654200	Weak transcription	Small Intestine	intestine
32	chr15:75641600-75659200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:75641600-75659600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr15:75641800-75643800	Enhancers	Dnd41	blood
35	chr15:75641800-75644000	ZNF genes & repeats	Primary B cells from cord blood	blood
36	chr15:75641800-75644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:75641800-75644400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:75641800-75644800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:75641800-75645000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:75641800-75645800	Weak transcription	Fetal Intestine Large	intestine
41	chr15:75641800-75646000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:75641800-75646000	Weak transcription	Esophagus	oesophagus
43	chr15:75641800-75646000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:75641800-75646200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:75641800-75646200	Weak transcription	NHEK	skin
46	chr15:75641800-75646600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:75641800-75647200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr15:75641800-75647400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:75641800-75647400	Weak transcription	Hela-S3	cervix
50	chr15:75641800-75648200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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