Variant report

Variant	rs924840
Chromosome Location	chr15:78731808-78731809
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:78587653..78594388-chr15:78727556..78733158,9	MCF-7	breast:
2	chr15:78731552..78733950-chr15:78743733..78745911,2	MCF-7	breast:
3	chr15:78730985..78732538-chr15:78840858..78843812,2	K562	blood:
4	chr15:78730901..78732444-chr7:139043987..139045989,2	MCF-7	breast:
5	chr15:78731227..78733467-chr3:64216080..64218992,2	MCF-7	breast:
6	chr15:78631296..78634136-chr15:78730282..78731921,2	MCF-7	breast:
7	chr15:78590258..78594216-chr15:78729143..78732539,8	K562	blood:
8	chr15:78730825..78732581-chr15:78754139..78756670,3	K562	blood:
9	chr15:78728558..78732848-chr15:78754139..78757790,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000136381	Chromatin interaction
ENSG00000146963	Chromatin interaction
ENSG00000273391	Chromatin interaction
ENSG00000140395	Chromatin interaction
ENSG00000166426	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10851906	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072763	0.88[EUR][1000 genomes]
rs11072766	0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12101809	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16969894	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2036529	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2036533	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568483	0.80[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568485	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568488	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568490	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568493	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568497	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568498	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2568499	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2656055	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2656056	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2656069	0.80[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656070	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2656071	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656072	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2656073	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656074	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28480606	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28511883	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28602670	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2869032	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2869045	0.80[ASW][hapmap];0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2915695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2938671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2938674	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2958719	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35031105	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4887053	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5019044	0.93[CEU][hapmap];0.86[YRI][hapmap]
rs7174190	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7174348	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs958025	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9672608	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs924840	IREB2	cis	lesional skin	skin_eQTL
rs924840	FAH	cis	parietal	SCAN
rs924840	PARP6	cis	cerebellum	SCAN
rs924840	CHRNA5	cis	cerebellum	SCAN
rs924840	PSMA4	cis	parietal	SCAN
rs924840	COX5A	cis	parietal	SCAN
rs924840	PSMA4	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78729600-78732000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:78729600-78732000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr15:78729600-78732000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr15:78729600-78732000	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr15:78729600-78732000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr15:78729600-78732000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:78729600-78732000	Active TSS	Psoas Muscle	Psoas
8	chr15:78729600-78732000	Active TSS	Right Atrium	heart
9	chr15:78729600-78732200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr15:78729600-78732200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr15:78729600-78732200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr15:78729800-78732000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:78729800-78732000	Active TSS	A549	lung
14	chr15:78730000-78732000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr15:78730000-78732000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:78730000-78732000	Active TSS	GM12878-XiMat	blood
17	chr15:78730000-78732000	Active TSS	HSMMtube	muscle
18	chr15:78730000-78732000	Active TSS	NHLF	lung
19	chr15:78730000-78732200	Active TSS	NHDF-Ad	bronchial
20	chr15:78730200-78732000	Active TSS	HepG2	liver
21	chr15:78731000-78732000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr15:78731000-78732000	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr15:78731000-78732200	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr15:78731200-78732000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr15:78731200-78732000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:78731200-78732000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr15:78731400-78732000	Enhancers	Primary B cells from peripheral blood	blood
28	chr15:78731400-78732000	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr15:78731400-78732000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:78731400-78732000	Flanking Active TSS	Liver	Liver
31	chr15:78731400-78732000	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr15:78731400-78732000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr15:78731400-78732000	Enhancers	Small Intestine	intestine
34	chr15:78731400-78732000	Flanking Active TSS	Osteobl	bone
35	chr15:78731400-78732200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:78731400-78732200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr15:78731400-78732200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:78731400-78732200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:78731400-78732200	Flanking Active TSS	Fetal Kidney	kidney
40	chr15:78731400-78732200	Flanking Active TSS	Hela-S3	cervix
41	chr15:78731400-78732200	Flanking Active TSS	HUVEC	blood vessel
42	chr15:78731400-78734200	Weak transcription	Gastric	stomach
43	chr15:78731400-78734400	Weak transcription	Spleen	Spleen
44	chr15:78731400-78745400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr15:78731600-78732000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:78731600-78732000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr15:78731600-78732000	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr15:78731600-78732000	Flanking Active TSS	Fetal Brain Female	brain
49	chr15:78731600-78732000	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr15:78731600-78732000	Flanking Active TSS	Fetal Lung	lung

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