Variant report

Variant	rs3814281
Chromosome Location	chr15:83499766-83499767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:116661921..116663439-chr15:83498136..83501074,2	MCF-7	breast:
2	chr15:83497773..83500500-chr15:83501869..83504757,2	K562	blood:
3	chr15:83497018..83500985-chr15:83502247..83506806,4	MCF-7	breast:
4	chr15:83477460..83480587-chr15:83496112..83502372,6	K562	blood:
5	chr15:83484279..83486201-chr15:83497779..83499925,2	K562	blood:
6	chr15:83495199..83497362-chr15:83499457..83501013,2	K562	blood:
7	chr15:83495862..83497428-chr15:83499513..83501800,2	K562	blood:
8	chr15:83478452..83480034-chr15:83499455..83501748,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000156232	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1105287	0.95[GIH][hapmap];0.85[TSI][hapmap]
rs11631033	0.95[GIH][hapmap]
rs11631378	0.83[ASN][1000 genomes]
rs11635357	0.95[GIH][hapmap]
rs11637448	0.95[GIH][hapmap];0.81[TSI][hapmap]
rs11637563	0.83[ASN][1000 genomes]
rs11857233	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1256430	0.87[GIH][hapmap]
rs12907810	0.86[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1553886	0.95[GIH][hapmap];0.85[TSI][hapmap]
rs17158255	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2137052	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34291804	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34337936	0.86[ASN][1000 genomes]
rs35407574	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35590674	0.83[ASN][1000 genomes]
rs35852340	0.85[ASN][1000 genomes]
rs35989256	0.94[ASN][1000 genomes]
rs3814282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132210	0.95[GIH][hapmap];0.85[TSI][hapmap]
rs4779061	0.95[GIH][hapmap];0.85[TSI][hapmap]
rs57252413	0.83[ASN][1000 genomes]
rs72753973	0.83[AFR][1000 genomes];0.82[ASN][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	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	nsv977748	chr15:83496161-83500241	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3814281	PSMA4	cis	parietal	SCAN
rs3814281	C15orf26	cis	parietal	SCAN
rs3814281	BCL7C	trans	cerebellum	SCAN
rs3814281	RASGRF1	cis	cerebellum	SCAN
rs3814281	WHAMM	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83479600-83504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:83479800-83504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:83480000-83501600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:83480400-83500600	Weak transcription	Stomach Mucosa	stomach
5	chr15:83480400-83507000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:83481000-83499800	Weak transcription	Fetal Heart	heart
7	chr15:83481200-83507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:83481400-83500800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:83481400-83507000	Strong transcription	Placenta	Placenta
10	chr15:83481600-83500800	Strong transcription	Fetal Thymus	thymus
11	chr15:83481600-83507000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr15:83481800-83500000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:83481800-83506200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:83481800-83507000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr15:83481800-83507600	Strong transcription	Adipose Nuclei	Adipose
16	chr15:83482000-83500000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:83482000-83500200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr15:83482000-83506800	Strong transcription	Fetal Intestine Large	intestine
19	chr15:83482000-83507000	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:83482200-83500200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr15:83482200-83507000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr15:83482600-83500200	Strong transcription	Fetal Lung	lung
23	chr15:83482800-83500400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:83482800-83506800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr15:83483200-83507400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:83484800-83505400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr15:83485200-83500600	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr15:83485400-83500600	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:83487800-83500200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:83488400-83505000	Strong transcription	Fetal Stomach	stomach
31	chr15:83488800-83501800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr15:83489200-83500200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:83489200-83500800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:83489200-83506800	Weak transcription	Fetal Brain Male	brain
35	chr15:83489800-83499800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:83491000-83500600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:83491000-83500600	Strong transcription	HSMM	muscle
38	chr15:83491000-83508000	Strong transcription	Thymus	Thymus
39	chr15:83491200-83506400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr15:83491200-83507400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr15:83491400-83500200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:83491400-83500200	Strong transcription	NH-A	brain
43	chr15:83491400-83505000	Strong transcription	Spleen	Spleen
44	chr15:83491400-83506600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:83491400-83507400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:83491400-83507400	Strong transcription	Fetal Muscle Leg	muscle
47	chr15:83491400-83508200	Strong transcription	Left Ventricle	heart
48	chr15:83491600-83500200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:83491600-83500200	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr15:83491600-83500400	Strong transcription	Osteobl	bone

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