Variant report

Variant	rs11259951
Chromosome Location	chr15:83482318-83482319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr15:83482209-83482406	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr15:83481184-83482387	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:83480184..83483063-chr15:83673551..83675141,2	K562	blood:
2	chr15:83482141..83484668-chr15:83493605..83496419,2	MCF-7	breast:
3	chr15:83476157..83479071-chr15:83480775..83482878,2	K562	blood:
4	chr15:83481406..83484295-chr15:83488515..83491028,2	MCF-7	breast:
5	chr15:83313427..83317808-chr15:83477553..83483000,6	K562	blood:

No data

Variant related genes	Relation type
WHAMM	TF binding region
ENSG00000214575	Chromatin interaction
ENSG00000156232	Chromatin interaction
ENSG00000259462	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11635618	0.93[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs11856316	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11856878	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12903359	0.91[ASN][1000 genomes]
rs12905388	0.81[CEU][hapmap];0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs12910606	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17158263	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1828510	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2046071	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs2379994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34541883	0.90[ASN][1000 genomes]
rs35788008	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4778691	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7174089	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7182990	0.90[ASN][1000 genomes]
rs8042254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9806482	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv977747	chr15:83479370-83496161	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	nsv9288	chr15:83479484-83496828	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11259951	WHAMM	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83479400-83482400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:83479600-83485800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:83479600-83504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:83479800-83483200	Weak transcription	Gastric	stomach
5	chr15:83479800-83504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:83480000-83482800	Weak transcription	Fetal Brain Female	brain
7	chr15:83480000-83485600	Weak transcription	Esophagus	oesophagus
8	chr15:83480000-83497000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:83480000-83501600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:83480200-83484000	Weak transcription	Fetal Brain Male	brain
11	chr15:83480200-83485400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:83480200-83487400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:83480200-83489000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:83480400-83482400	Weak transcription	Fetal Stomach	stomach
15	chr15:83480400-83482400	Weak transcription	HSMM	muscle
16	chr15:83480400-83482600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:83480400-83482800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:83480400-83484000	Weak transcription	Colonic Mucosa	Colon
19	chr15:83480400-83484200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:83480400-83484600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:83480400-83485400	Weak transcription	Thymus	Thymus
22	chr15:83480400-83485800	Weak transcription	Aorta	Aorta
23	chr15:83480400-83487400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:83480400-83488400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr15:83480400-83493600	Weak transcription	Brain Germinal Matrix	brain
26	chr15:83480400-83500600	Weak transcription	Stomach Mucosa	stomach
27	chr15:83480400-83507000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr15:83480600-83482600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:83481000-83482400	Weak transcription	Brain Anterior Caudate	brain
30	chr15:83481000-83482400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:83481000-83482400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:83481000-83482400	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr15:83481000-83482400	Weak transcription	HMEC	breast
34	chr15:83481000-83482400	Weak transcription	NHEK	skin
35	chr15:83481000-83482600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:83481000-83482600	Weak transcription	Fetal Lung	lung
37	chr15:83481000-83482800	Weak transcription	Brain Angular Gyrus	brain
38	chr15:83481000-83484000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:83481000-83484000	Weak transcription	Brain Substantia Nigra	brain
40	chr15:83481000-83484800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:83481000-83485400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr15:83481000-83485800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr15:83481000-83499800	Weak transcription	Fetal Heart	heart
44	chr15:83481200-83482800	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr15:83481200-83487400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:83481200-83507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:83481400-83482400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:83481400-83482600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:83481400-83482600	Weak transcription	Ovary	ovary
50	chr15:83481400-83482600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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