Variant report

Variant	rs2486271
Chromosome Location	chr15:45692634-45692635
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:45692606-45692896	HepG2	liver:	n/a	n/a
2	CTCF	chr15:45692520-45692670	AG10803	skin:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45597883..45600169-chr15:45691864..45693737,3	MCF-7	breast:
2	chr15:45682453..45684162-chr15:45690788..45693416,2	K562	blood:
3	chr11:67112594..67114538-chr15:45691318..45694198,2	MCF-7	breast:
4	chr15:45685120..45688238-chr15:45691728..45694195,3	MCF-7	breast:
5	chr15:45490969..45492554-chr15:45691129..45692848,2	K562	blood:
6	chr15:45598248..45599758-chr15:45691889..45693667,2	MCF-7	breast:
7	chr15:45690046..45692926-chr15:45693483..45695638,2	MCF-7	breast:

No data

Variant related genes	Relation type
SPATA5L1	TF binding region
GATM	TF binding region
ENSG00000171763	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000259932	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1055395	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070455	1.00[EUR][1000 genomes]
rs1145072	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145073	0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145075	0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs1145082	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145092	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145094	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145099	0.86[YRI][hapmap]
rs1153848	0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs1153850	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153851	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153856	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153859	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1346265	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1403319	1.00[EUR][1000 genomes]
rs1464558	1.00[EUR][1000 genomes]
rs1706775	1.00[EUR][1000 genomes]
rs1706782	1.00[EUR][1000 genomes]
rs1706783	1.00[EUR][1000 genomes]
rs1706784	1.00[EUR][1000 genomes]
rs1706786	1.00[EUR][1000 genomes]
rs1706788	1.00[EUR][1000 genomes]
rs1706789	1.00[EUR][1000 genomes]
rs1706790	1.00[EUR][1000 genomes]
rs1706794	1.00[EUR][1000 genomes]
rs1706795	1.00[EUR][1000 genomes]
rs1706796	1.00[EUR][1000 genomes]
rs1706797	1.00[EUR][1000 genomes]
rs1706800	0.83[YRI][hapmap]
rs1706801	0.89[YRI][hapmap]
rs1719242	1.00[EUR][1000 genomes]
rs1719249	1.00[EUR][1000 genomes]
rs1834686	0.83[AMR][1000 genomes]
rs1874318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2217121	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2413765	0.83[AMR][1000 genomes]
rs2433603	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433604	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433605	0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433609	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433610	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453544	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453547	0.83[AMR][1000 genomes]
rs2461704	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467852	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467855	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467857	0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467859	0.83[AMR][1000 genomes]
rs2486273	0.86[AFR][1000 genomes]
rs2486289	0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2486290	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2668740	1.00[EUR][1000 genomes]
rs2687513	1.00[EUR][1000 genomes]
rs57553327	1.00[EUR][1000 genomes]
rs7163395	1.00[EUR][1000 genomes]
rs7163751	1.00[EUR][1000 genomes]
rs7164252	1.00[EUR][1000 genomes]
rs7169175	1.00[EUR][1000 genomes]
rs7173541	1.00[EUR][1000 genomes]
rs7179186	1.00[EUR][1000 genomes]
rs7179844	1.00[EUR][1000 genomes]
rs74009622	1.00[EUR][1000 genomes]
rs8024550	0.83[AMR][1000 genomes]
rs8028061	1.00[EUR][1000 genomes]
rs8033329	1.00[EUR][1000 genomes]
rs8040380	1.00[EUR][1000 genomes]
rs9806260	1.00[EUR][1000 genomes]
rs9972564	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45679000-45693800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:45682800-45693800	Weak transcription	Brain Angular Gyrus	brain
3	chr15:45685600-45692800	Weak transcription	GM12878-XiMat	blood
4	chr15:45686800-45693600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:45687200-45693800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:45687400-45693200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:45688400-45693400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:45688800-45693600	Weak transcription	Brain Substantia Nigra	brain
9	chr15:45689800-45693200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:45689800-45693200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:45690800-45693200	Enhancers	Liver	Liver
12	chr15:45691400-45693000	Enhancers	HepG2	liver
13	chr15:45691600-45693400	Enhancers	Fetal Intestine Small	intestine
14	chr15:45691800-45693000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:45692000-45693000	Weak transcription	Fetal Intestine Large	intestine
16	chr15:45692000-45693200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:45692000-45693400	Weak transcription	Brain Anterior Caudate	brain
18	chr15:45692000-45693400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:45692000-45693400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:45692000-45693400	Weak transcription	Fetal Brain Female	brain
21	chr15:45692000-45693600	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:45692000-45693800	Weak transcription	Small Intestine	intestine
23	chr15:45692200-45693400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:45692200-45693400	Weak transcription	Stomach Mucosa	stomach
25	chr15:45692200-45693600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr15:45692200-45693800	Weak transcription	Pancreas	Pancrea
27	chr15:45692600-45693000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:45692600-45693000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:45692600-45693200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr15:45692600-45693200	Enhancers	Duodenum Mucosa	Duodenum

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