Variant report

Variant	rs16958770
Chromosome Location	chr15:34393214-34393215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr15:34393074-34394800	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr15:34393004-34394647	MCF10A-Er-Src	breast:	n/a	n/a
3	HCFC1	chr15:34392947-34394803	Hela-S3	cervix:	n/a	n/a
4	MXI1	chr15:34392820-34395203	SK-N-SH	brain:	n/a	chr15:34393499-34393508

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:34391885..34395742-chr15:34500701..34502399,4	K562	blood:
2	chr15:34392506..34394195-chr15:34653164..34655913,2	MCF-7	breast:
3	chr15:34391770..34396248-chr15:34515474..34518631,5	K562	blood:
4	chr15:34391496..34393371-chr15:34874535..34876931,2	K562	blood:
5	chr15:34393027..34397233-chr15:34658612..34660877,5	K562	blood:
6	chr15:34392784..34394847-chr15:34629052..34631553,2	K562	blood:
7	chr15:34393027..34394938-chr15:34659377..34661190,2	K562	blood:
8	chr15:34391225..34395745-chr15:34498845..34504196,8	K562	blood:
9	chr15:34392855..34396101-chr15:34515904..34518783,5	MCF-7	breast:

No data

Variant related genes	Relation type
PGBD4	TF binding region
ENSG00000176454	Chromatin interaction
ENSG00000215252	Chromatin interaction
ENSG00000140199	Chromatin interaction
ENSG00000134152	Chromatin interaction
ENSG00000128463	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11072954	0.93[EUR][1000 genomes]
rs11634597	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11853879	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11856158	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12592547	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12592856	0.85[EUR][1000 genomes]
rs12594048	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12903028	0.85[EUR][1000 genomes]
rs1436923	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1865925	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339374	0.85[EUR][1000 genomes]
rs2568532	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576308	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576310	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28376576	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3794593	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4288968	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4468578	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4780214	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4780215	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4780216	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs522397	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs56310728	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57205845	0.85[ASN][1000 genomes]
rs623941	0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6495519	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7161835	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7163226	0.96[EUR][1000 genomes]
rs7182085	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs721122	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73374335	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028703	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038259	1.00[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1035579	chr15:34363159-34501115	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34380200-34393400	Weak transcription	Gastric	stomach
2	chr15:34381200-34393400	Weak transcription	Pancreas	Pancrea
3	chr15:34391800-34394800	Active TSS	GM12878-XiMat	blood
4	chr15:34392200-34393600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:34392200-34394600	Active TSS	Rectal Smooth Muscle	rectum
6	chr15:34392400-34393400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:34392400-34393600	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr15:34392400-34394800	Active TSS	K562	blood
9	chr15:34392400-34394800	Active TSS	NHLF	lung
10	chr15:34392400-34395400	Active TSS	Psoas Muscle	Psoas
11	chr15:34392600-34393400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr15:34392600-34393400	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr15:34392600-34393400	Flanking Active TSS	Fetal Brain Female	brain
14	chr15:34392600-34393400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr15:34392600-34393400	Weak transcription	Spleen	Spleen
16	chr15:34392600-34393400	Flanking Active TSS	Osteobl	bone
17	chr15:34392600-34393600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr15:34392600-34393600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:34392600-34393600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr15:34392600-34393600	Flanking Active TSS	HUVEC	blood vessel
21	chr15:34392600-34393800	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr15:34392600-34393800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr15:34392600-34393800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:34392600-34393800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr15:34392600-34394600	Active TSS	Stomach Smooth Muscle	stomach
26	chr15:34392600-34395000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:34392600-34395000	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr15:34392600-34395000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:34392600-34395200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:34392800-34393400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr15:34392800-34393400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr15:34392800-34393400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr15:34392800-34393400	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr15:34392800-34393400	Flanking Active TSS	Fetal Brain Male	brain
35	chr15:34392800-34393400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr15:34392800-34393400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr15:34392800-34393600	Flanking Active TSS	Liver	Liver
38	chr15:34392800-34393600	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr15:34392800-34393800	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr15:34392800-34393800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr15:34392800-34394600	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr15:34392800-34394600	Active TSS	Fetal Kidney	kidney
43	chr15:34392800-34394800	Active TSS	Fetal Intestine Small	intestine
44	chr15:34392800-34394800	Active TSS	Fetal Muscle Leg	muscle
45	chr15:34392800-34394800	Active TSS	Right Atrium	heart
46	chr15:34392800-34394800	Active TSS	HSMMtube	muscle
47	chr15:34392800-34395200	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr15:34392800-34395200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:34392800-34395400	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr15:34392800-34395600	Active TSS	ES-I3 Cell Line	embryonic stem cell

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