Variant report

Variant	rs4310817
Chromosome Location	chr15:75627638-75627639
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIX5	chr15:75627612-75628991	A549	lung:	n/a	chr15:75627639-75627648
2	POLR2A	chr15:75627584-75628875	PFSK-1	brain:	n/a	n/a
3	MXI1	chr15:75627573-75629389	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr15:75627633-75627953	SH-SY5Y	brain:	n/a	chr15:75627786-75627802
5	HCFC1	chr15:75627403-75629468	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75626715..75630609-chr15:75659083..75662163,7	K562	blood:
2	chr15:75626956..75629637-chr15:75642872..75644867,2	MCF-7	breast:
3	chr15:75626774..75630064-chr15:75654261..75656966,3	K562	blood:
4	chr15:75626851..75629633-chr15:75646566..75649228,2	K562	blood:
5	chr15:75626494..75629832-chr15:75639090..75642248,3	MCF-7	breast:
6	chr15:75627175..75629335-chr15:75660124..75661831,2	MCF-7	breast:
7	chr15:75246342..75249068-chr15:75626976..75630362,3	K562	blood:

No data

Variant related genes	Relation type
COMMD4	TF binding region
ENSG00000178718	Chromatin interaction
ENSG00000260591	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000140398	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11634109	0.90[EUR][1000 genomes]
rs1809714	0.93[EUR][1000 genomes]
rs1984586	0.92[EUR][1000 genomes]
rs1984587	0.90[EUR][1000 genomes]
rs3866545	0.92[EUR][1000 genomes]
rs4886684	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55653892	0.93[EUR][1000 genomes]
rs56164452	0.93[EUR][1000 genomes]
rs59084522	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7164167	0.94[EUR][1000 genomes]
rs7164429	0.94[EUR][1000 genomes]
rs7166436	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7166852	0.90[EUR][1000 genomes]
rs7167401	0.92[EUR][1000 genomes]
rs7183520	0.91[EUR][1000 genomes]
rs73435015	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73435089	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73436803	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8031650	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9673084	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv977736	chr15:75509295-75632679	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4310817	MAN2C1	cis	Whole Blood	GTEx
rs4310817	SNUPN	cis	Thyroid	GTEx
rs4310817	MAN2C1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75618000-75628000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:75623200-75628400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:75625800-75628000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:75627400-75627800	Enhancers	Primary T cells from cord blood	blood
5	chr15:75627400-75627800	Enhancers	Primary hematopoietic stem cells	blood
6	chr15:75627400-75627800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr15:75627400-75627800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:75627400-75627800	Enhancers	NHEK	skin
9	chr15:75627400-75628000	Flanking Active TSS	Hela-S3	cervix
10	chr15:75627600-75627800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:75627600-75627800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr15:75627600-75627800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr15:75627600-75627800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr15:75627600-75627800	Active TSS	Primary B cells from cord blood	blood
15	chr15:75627600-75627800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr15:75627600-75627800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:75627600-75627800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr15:75627600-75627800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr15:75627600-75627800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr15:75627600-75627800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr15:75627600-75627800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr15:75627600-75627800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:75627600-75627800	Enhancers	Liver	Liver
24	chr15:75627600-75627800	Enhancers	Brain Anterior Caudate	brain
25	chr15:75627600-75627800	Enhancers	Brain Germinal Matrix	brain
26	chr15:75627600-75627800	Enhancers	Brain Hippocampus Middle	brain
27	chr15:75627600-75627800	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr15:75627600-75627800	Enhancers	Duodenum Mucosa	Duodenum
29	chr15:75627600-75627800	Active TSS	Fetal Brain Male	brain
30	chr15:75627600-75627800	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr15:75627600-75627800	Enhancers	Fetal Thymus	thymus
32	chr15:75627600-75627800	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr15:75627600-75627800	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr15:75627600-75627800	Enhancers	Thymus	Thymus
35	chr15:75627600-75627800	Active TSS	GM12878-XiMat	blood
36	chr15:75627600-75627800	Enhancers	HMEC	breast
37	chr15:75627600-75627800	Enhancers	HSMMtube	muscle
38	chr15:75627600-75627800	Enhancers	HUVEC	blood vessel
39	chr15:75627600-75627800	Enhancers	NHDF-Ad	bronchial
40	chr15:75627600-75627800	Enhancers	Osteobl	bone
41	chr15:75627600-75628000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:75627600-75628000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:75627600-75628000	Enhancers	Primary B cells from peripheral blood	blood
44	chr15:75627600-75628000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr15:75627600-75628000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr15:75627600-75628000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:75627600-75628000	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr15:75627600-75628000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr15:75627600-75628000	Flanking Active TSS	Fetal Heart	heart
50	chr15:75627600-75628000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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