Variant report

Variant	rs12593834
Chromosome Location	chr15:92555140-92555141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:92552941..92555827-chr15:92557594..92560539,2	MCF-7	breast:
2	chr15:92552040..92555185-chr15:92557169..92559357,3	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12439818	0.85[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs12441537	0.87[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.90[ASN][1000 genomes]
rs12915872	0.80[CHD][hapmap]
rs1400784	0.83[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs17695404	0.90[ASN][1000 genomes]
rs4984324	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4984325	1.00[GIH][hapmap]
rs7165226	0.82[CHD][hapmap];0.81[GIH][hapmap]
rs7171137	0.84[CHD][hapmap];0.94[JPT][hapmap]
rs7174192	0.89[JPT][hapmap]
rs72630490	0.91[ASN][1000 genomes]
rs7498017	1.00[JPT][hapmap];0.91[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12593834	SNHG9	trans	lymphoblastoid	seeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92549600-92555400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr15:92550400-92556200	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr15:92550800-92562600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:92551200-92556400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr15:92551200-92557400	Enhancers	Ovary	ovary
6	chr15:92551600-92556000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:92552200-92559000	Enhancers	Left Ventricle	heart
8	chr15:92552800-92561800	Weak transcription	Psoas Muscle	Psoas
9	chr15:92553000-92555200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr15:92553000-92555200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:92553400-92555200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:92553400-92555800	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr15:92553800-92555200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:92553800-92555400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:92554000-92555800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr15:92554000-92555800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr15:92554000-92556800	Enhancers	Pancreas	Pancrea
18	chr15:92554000-92556800	Enhancers	Right Ventricle	heart
19	chr15:92554000-92559200	Enhancers	Brain Substantia Nigra	brain
20	chr15:92554200-92555200	Enhancers	Primary T cells from cord blood	blood
21	chr15:92554200-92555200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr15:92554200-92555600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr15:92554200-92555600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr15:92554200-92555800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr15:92554200-92555800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr15:92554200-92555800	Enhancers	Esophagus	oesophagus
27	chr15:92554200-92556000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr15:92554200-92556600	Enhancers	Spleen	Spleen
29	chr15:92554200-92556800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:92554200-92559200	Enhancers	Brain Angular Gyrus	brain
31	chr15:92554200-92566200	Enhancers	Right Atrium	heart
32	chr15:92554400-92555200	Weak transcription	Fetal Brain Female	brain
33	chr15:92554400-92555200	Enhancers	NHEK	skin
34	chr15:92554400-92555400	Enhancers	Stomach Smooth Muscle	stomach
35	chr15:92554600-92555600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr15:92554800-92555200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:92554800-92555200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr15:92554800-92555200	Enhancers	HMEC	breast
39	chr15:92554800-92555400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr15:92554800-92555600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:92554800-92555600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:92554800-92555600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:92554800-92555600	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr15:92554800-92555600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr15:92554800-92555800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr15:92554800-92555800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr15:92554800-92555800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:92554800-92555800	Enhancers	A549	lung
49	chr15:92554800-92555800	Enhancers	Hela-S3	cervix
50	chr15:92554800-92556400	Enhancers	Primary hematopoietic stem cells	blood

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