Variant report

Variant	rs12912997
Chromosome Location	chr15:92550563-92550564
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:92538879..92541331-chr15:92548247..92550624,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10468145	1.00[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12593984	0.87[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs12899673	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs12903900	1.00[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12904266	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12905838	0.86[CEU][hapmap]
rs12905912	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908689	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912272	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12913189	0.83[JPT][hapmap]
rs1983351	0.83[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs62011574	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6496886	0.93[ASN][1000 genomes]
rs7166185	0.83[JPT][hapmap]
rs7178378	0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7181178	0.83[JPT][hapmap]
rs7495052	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs8040010	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	nsv1048635	chr15:92073294-92557339	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534110	chr15:92397220-92592961	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv904498	chr15:92545284-92558234	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12912997	DET1	cis	parietal	SCAN
rs12912997	ACAN	cis	parietal	SCAN
rs12912997	FES	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92498200-92555000	Weak transcription	Gastric	stomach
2	chr15:92527400-92551400	Weak transcription	Aorta	Aorta
3	chr15:92538200-92554800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr15:92543000-92552400	Weak transcription	Pancreas	Pancrea
5	chr15:92543600-92550800	Enhancers	Brain Substantia Nigra	brain
6	chr15:92544200-92554800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:92544400-92554800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:92544800-92551200	Weak transcription	Ovary	ovary
9	chr15:92544800-92552400	Weak transcription	Spleen	Spleen
10	chr15:92544800-92554200	Weak transcription	Fetal Brain Female	brain
11	chr15:92544800-92554800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:92545400-92554800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:92545600-92552400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:92546400-92551800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr15:92546800-92551000	Enhancers	Brain Hippocampus Middle	brain
16	chr15:92547000-92553400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:92547200-92552000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr15:92547400-92552400	Weak transcription	Psoas Muscle	Psoas
19	chr15:92547400-92553000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:92547400-92553000	Weak transcription	Right Ventricle	heart
21	chr15:92547600-92551400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr15:92547600-92552400	Weak transcription	Lung	lung
23	chr15:92547600-92552600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:92547600-92555000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:92548200-92554200	Weak transcription	Primary T cells from cord blood	blood
26	chr15:92548400-92550800	Enhancers	Brain Anterior Caudate	brain
27	chr15:92548400-92551400	Weak transcription	Fetal Heart	heart
28	chr15:92548600-92551800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr15:92549000-92552400	Weak transcription	Esophagus	oesophagus
30	chr15:92549000-92554800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:92549200-92550800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr15:92549200-92550800	Enhancers	Brain Cingulate Gyrus	brain
33	chr15:92549200-92554200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:92549200-92554600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr15:92549200-92555000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:92549400-92550600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr15:92549400-92550600	Enhancers	Brain Angular Gyrus	brain
38	chr15:92549400-92551000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:92549400-92551200	Weak transcription	Left Ventricle	heart
40	chr15:92549400-92551600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:92549400-92552400	Weak transcription	Right Atrium	heart
42	chr15:92549400-92554800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:92549600-92553400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:92549600-92554200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:92549600-92554200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:92549600-92555400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:92549800-92551200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:92549800-92553400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr15:92549800-92554200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr15:92549800-92555000	Weak transcription	H9 Cell Line	embryonic stem cell

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