Variant report

Variant	rs2088858
Chromosome Location	chr15:82474749-82474750
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	chr15:82472620..82475056-chr15:82476421..82478115,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1045508	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11073035	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1174543	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1174546	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11855089	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11855144	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11857208	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12443224	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12905578	0.87[ASN][1000 genomes]
rs13380317	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13380319	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1392976	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1501371	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1501372	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1846911	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2047678	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2455717	0.83[EUR][1000 genomes]
rs28540744	0.89[ASN][1000 genomes]
rs2867577	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2867579	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3858954	0.88[ASN][1000 genomes]
rs4270132	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4344697	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4778982	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495642	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6495643	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495647	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7164362	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166570	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7169961	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173339	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7173852	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7176075	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7180584	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7181655	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8025353	0.86[ASN][1000 genomes]
rs8033050	0.89[ASN][1000 genomes]
rs8033831	0.82[EUR][1000 genomes]
rs8037224	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8041868	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8041924	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8042464	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8043108	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs867370	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs867371	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs881308	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9944197	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457212	chr15:82454283-82573255	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv570243	chr15:82454283-82573255	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv457213	chr15:82456227-82573255	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv570244	chr15:82456227-82573255	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv570245	chr15:82456227-82591082	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1041040	chr15:82465124-82606410	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1801737	chr15:82468455-82589044	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2088858	GOLGA6L10	cis	Esophagus Mucosa	GTEx
rs2088858	RP13-608F4.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82432600-82476400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:82432600-82552800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr15:82444600-82495800	Weak transcription	Fetal Intestine Small	intestine
4	chr15:82455400-82475200	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:82455400-82475200	Weak transcription	Pancreas	Pancrea
6	chr15:82455600-82475200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:82456000-82475800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:82456000-82475800	Weak transcription	Lung	lung
9	chr15:82456000-82510000	Weak transcription	Thymus	Thymus
10	chr15:82456200-82475200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:82456200-82475600	Weak transcription	Fetal Brain Female	brain
12	chr15:82456400-82475200	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:82456400-82475200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:82456400-82475400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:82456400-82475800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr15:82456400-82480600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:82456400-82487000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr15:82456400-82502200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr15:82456400-82502400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr15:82456400-82502600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:82456400-82502800	Weak transcription	Gastric	stomach
22	chr15:82456400-82505400	Weak transcription	Dnd41	blood
23	chr15:82456400-82505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:82456400-82505600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:82456600-82478600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:82456600-82497400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:82456800-82475200	Weak transcription	Liver	Liver
28	chr15:82456800-82509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:82458200-82504800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:82458600-82475600	Weak transcription	GM12878-XiMat	blood
31	chr15:82458600-82479200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:82458800-82502800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:82460800-82475200	Weak transcription	Primary T cells from cord blood	blood
34	chr15:82462000-82475800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:82462000-82505800	Weak transcription	Primary B cells from cord blood	blood
36	chr15:82464000-82475400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:82464000-82494800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:82464200-82476600	Weak transcription	Hela-S3	cervix
39	chr15:82465000-82510000	Weak transcription	Placenta	Placenta
40	chr15:82467400-82475200	Weak transcription	Brain Substantia Nigra	brain
41	chr15:82469600-82475200	Weak transcription	Brain Anterior Caudate	brain
42	chr15:82470200-82476600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:82471000-82475200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:82471000-82475200	Weak transcription	Left Ventricle	heart
45	chr15:82471000-82475200	Weak transcription	Ovary	ovary
46	chr15:82471000-82475200	Weak transcription	Psoas Muscle	Psoas
47	chr15:82471000-82475200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr15:82471000-82475200	Weak transcription	HSMMtube	muscle
49	chr15:82471000-82475200	Weak transcription	NH-A	brain
50	chr15:82471000-82475400	Weak transcription	Fetal Heart	heart

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