Variant report

Variant	rs3803464
Chromosome Location	chr15:75654366-75654367
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75654091-75655643	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:75654017-75654680	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:75654032-75654484	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr15:75654298-75654660	K562	blood:	n/a	n/a
5	POLR2A	chr15:75654326-75654731	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:75654051-75655215	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:75650613-75655985	GM12892	blood:	n/a	n/a
8	POLR2A	chr15:75650366-75655745	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:75654019-75655810	A549	lung:	n/a	n/a
10	POLR2A	chr15:75654331-75655622	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr15:75654103-75654553	GM12892	blood:	n/a	n/a
12	POLR2A	chr15:75654042-75654417	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr15:75651531-75655942	GM12892	blood:	n/a	n/a
14	POLR2A	chr15:75654043-75654596	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:75654350-75655157	GM12891	blood:	n/a	n/a
16	POLR2A	chr15:75650465-75655849	K562	blood:	n/a	n/a
17	POLR2A	chr15:75654113-75655674	GM12891	blood:	n/a	n/a
18	POLR2A	chr15:75654253-75655835	K562	blood:	n/a	n/a
19	POLR2A	chr15:75654193-75655873	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75652075..75654560-chr15:75917811..75919944,2	K562	blood:
2	chr15:75626774..75630064-chr15:75654261..75656966,3	K562	blood:
3	chr15:75651898..75654769-chr15:75870111..75872338,3	MCF-7	breast:

No data

Variant related genes	Relation type
MAN2C1	TF binding region
ENSG00000140365	Chromatin interaction
ENSG00000169410	Chromatin interaction
ENSG00000169371	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11853961	0.95[AMR][1000 genomes]
rs11855799	1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11855880	1.00[EUR][1000 genomes]
rs11857278	0.95[AMR][1000 genomes]
rs3803465	0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61539627	0.89[AMR][1000 genomes]
rs7162587	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173927	0.95[AMR][1000 genomes]
rs7175454	0.95[AMR][1000 genomes]
rs7179862	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7180003	0.95[AMR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3803464	MAN2C1	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75641200-75655000	Weak transcription	K562	blood
2	chr15:75641400-75655400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:75641400-75658600	Weak transcription	HUVEC	blood vessel
4	chr15:75641600-75659200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:75641600-75659600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:75641800-75659600	Weak transcription	Fetal Heart	heart
7	chr15:75642000-75659600	Strong transcription	Fetal Intestine Small	intestine
8	chr15:75642200-75659800	Weak transcription	Fetal Brain Male	brain
9	chr15:75642400-75659800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:75643000-75659600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:75643200-75659800	Weak transcription	Right Atrium	heart
12	chr15:75643400-75654400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:75643400-75656800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:75643600-75656200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr15:75643800-75657000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:75644200-75659600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr15:75644200-75659800	Strong transcription	Fetal Stomach	stomach
18	chr15:75644400-75657600	Strong transcription	Gastric	stomach
19	chr15:75644400-75658000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:75644400-75658800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:75644400-75659600	Strong transcription	Colonic Mucosa	Colon
22	chr15:75644400-75659600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr15:75644400-75659800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:75644600-75659600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:75644800-75659600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:75645600-75659800	Strong transcription	Placenta	Placenta
27	chr15:75645800-75659600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:75645800-75659600	Strong transcription	Fetal Intestine Large	intestine
29	chr15:75645800-75660000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:75646000-75659200	Strong transcription	Brain Germinal Matrix	brain
31	chr15:75646000-75659200	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:75646000-75659400	Strong transcription	Primary T cells from cord blood	blood
33	chr15:75646000-75659400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:75646000-75659400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:75646000-75659800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:75646000-75659800	Strong transcription	NHLF	lung
37	chr15:75646000-75660200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:75646200-75659400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:75646200-75659400	Strong transcription	Esophagus	oesophagus
40	chr15:75646200-75659600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:75646200-75659600	Strong transcription	Adipose Nuclei	Adipose
42	chr15:75646200-75659600	Strong transcription	NHEK	skin
43	chr15:75646200-75659800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:75646200-75659800	Strong transcription	Fetal Muscle Leg	muscle
45	chr15:75646400-75659800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:75646600-75659400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr15:75646600-75659600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr15:75646800-75657600	Strong transcription	Right Ventricle	heart
49	chr15:75646800-75659400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr15:75646800-75659400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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