Variant report

Variant	rs12907810
Chromosome Location	chr15:83494051-83494052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83482141..83484668-chr15:83493605..83496419,2	MCF-7	breast:
2	chr15:83418952..83421075-chr15:83493113..83495192,2	K562	blood:

Variant related genes	Relation type
ENSG00000250988	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1105287	0.82[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs11631033	0.82[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs11631209	0.87[EUR][1000 genomes]
rs11631378	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11633676	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs11635290	0.88[EUR][1000 genomes]
rs11635357	0.82[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs11637448	0.95[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs11637563	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11857233	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256430	0.87[GIH][hapmap]
rs1256433	0.84[CEU][hapmap]
rs12914752	0.82[EUR][1000 genomes]
rs12917248	0.88[EUR][1000 genomes]
rs1553886	0.82[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs17158255	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2137052	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34291804	0.83[AMR][1000 genomes]
rs34337936	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35407574	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35590674	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35852340	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35989107	0.90[EUR][1000 genomes]
rs35989256	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3814281	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]
rs3814282	0.93[CHB][hapmap];0.90[JPT][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4132210	0.82[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs4779061	0.82[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs57252413	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60414706	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72753973	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12907810	RASGRF1	cis	cerebellum	SCAN
rs12907810	C15orf26	cis	parietal	SCAN
rs12907810	PSMA4	cis	parietal	SCAN
rs12907810	BCL7C	trans	cerebellum	SCAN
rs12907810	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	chr15:83480000-83497000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:83480000-83501600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:83480400-83500600	Weak transcription	Stomach Mucosa	stomach
6	chr15:83480400-83507000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:83481000-83499800	Weak transcription	Fetal Heart	heart
8	chr15:83481200-83507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:83481400-83500800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:83481400-83507000	Strong transcription	Placenta	Placenta
11	chr15:83481600-83500800	Strong transcription	Fetal Thymus	thymus
12	chr15:83481600-83507000	Strong transcription	Primary B cells from peripheral blood	blood
13	chr15:83481800-83496400	Strong transcription	Liver	Liver
14	chr15:83481800-83499400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:83481800-83500000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:83481800-83506200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:83481800-83507000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr15:83481800-83507600	Strong transcription	Adipose Nuclei	Adipose
19	chr15:83482000-83500000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:83482000-83500200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr15:83482000-83506800	Strong transcription	Fetal Intestine Large	intestine
22	chr15:83482000-83507000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:83482200-83500200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr15:83482200-83507000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr15:83482400-83495200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr15:83482400-83496600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:83482600-83500200	Strong transcription	Fetal Lung	lung
28	chr15:83482800-83500400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr15:83482800-83506800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr15:83483200-83507400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:83484800-83505400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr15:83485200-83500600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr15:83485400-83500600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:83485800-83496800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:83487800-83500200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:83488000-83494200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:83488000-83494400	Weak transcription	NHLF	lung
38	chr15:83488000-83496400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr15:83488400-83505000	Strong transcription	Fetal Stomach	stomach
40	chr15:83488800-83494600	Weak transcription	Brain Angular Gyrus	brain
41	chr15:83488800-83497000	Weak transcription	Psoas Muscle	Psoas
42	chr15:83488800-83501800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr15:83489000-83494800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:83489000-83497000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:83489200-83494600	Weak transcription	Brain Anterior Caudate	brain
46	chr15:83489200-83496600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:83489200-83500200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:83489200-83500800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:83489200-83506800	Weak transcription	Fetal Brain Male	brain
50	chr15:83489400-83494600	Weak transcription	A549	lung

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