Variant report

Variant	rs2456067
Chromosome Location	chr15:76581418-76581419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76580950..76582606-chr15:76603134..76604803,2	K562	blood:
2	chr15:76575843..76577535-chr15:76579301..76581844,2	MCF-7	breast:
3	chr15:76572935..76575613-chr15:76581006..76583216,3	K562	blood:
4	chr15:76580263..76582606-chr15:76602066..76604803,3	K562	blood:
5	chr15:76542765..76545706-chr15:76579953..76582422,2	K562	blood:
6	chr15:76573019..76575613-chr15:76581006..76583116,2	K562	blood:

Variant related genes	Relation type
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11858964	0.85[EUR][1000 genomes]
rs1801591	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1810348	0.87[EUR][1000 genomes]
rs1914816	0.89[ASN][1000 genomes]
rs2291449	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2456027	0.89[ASN][1000 genomes]
rs2456033	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2456040	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2456042	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2456047	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2456054	0.89[AMR][1000 genomes]
rs2456063	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2456066	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2456070	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2456072	0.89[ASN][1000 genomes]
rs2456074	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2456075	0.89[ASN][1000 genomes]
rs2456078	0.89[ASN][1000 genomes]
rs2460146	0.89[ASN][1000 genomes]
rs2460151	0.89[ASN][1000 genomes]
rs2460153	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460158	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2469211	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2469212	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2469214	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469215	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2469216	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2469533	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2469538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469539	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469544	0.82[ASN][1000 genomes]
rs2469552	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2469564	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469568	0.94[AMR][1000 genomes]
rs2469573	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2938691	0.89[ASN][1000 genomes]
rs2956875	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957037	0.89[ASN][1000 genomes]
rs2959846	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4489970	0.87[EUR][1000 genomes]
rs4886490	0.87[EUR][1000 genomes]
rs6495200	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7180257	0.85[EUR][1000 genomes]
rs8042255	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs874223	0.87[EUR][1000 genomes]
rs874224	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2456067	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2456067	ISL2	cis	Whole Blood	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76555800-76586000	Weak transcription	Stomach Mucosa	stomach
2	chr15:76556800-76594600	Weak transcription	Esophagus	oesophagus
3	chr15:76557000-76582800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:76558000-76603000	Weak transcription	Aorta	Aorta
5	chr15:76560000-76582400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:76561000-76587600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:76562000-76591600	Weak transcription	Small Intestine	intestine
8	chr15:76562600-76586000	Weak transcription	Brain Angular Gyrus	brain
9	chr15:76563000-76581800	Weak transcription	Fetal Brain Male	brain
10	chr15:76563000-76586400	Weak transcription	Fetal Heart	heart
11	chr15:76563200-76590800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:76567600-76581800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:76568800-76581600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:76569000-76585200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:76569000-76586400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr15:76569200-76581600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr15:76569400-76583600	Strong transcription	Hela-S3	cervix
18	chr15:76569400-76585000	Strong transcription	Fetal Intestine Large	intestine
19	chr15:76569800-76591600	Weak transcription	Spleen	Spleen
20	chr15:76571200-76586400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:76572000-76581600	Strong transcription	Placenta	Placenta
22	chr15:76572600-76585800	Weak transcription	Brain Anterior Caudate	brain
23	chr15:76573200-76592200	Weak transcription	Fetal Kidney	kidney
24	chr15:76573200-76593200	Weak transcription	Right Ventricle	heart
25	chr15:76574600-76585200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:76574800-76582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:76574800-76590600	Weak transcription	Ovary	ovary
28	chr15:76574800-76591600	Weak transcription	Gastric	stomach
29	chr15:76574800-76591600	Weak transcription	Lung	lung
30	chr15:76574800-76601400	Weak transcription	Pancreas	Pancrea
31	chr15:76574800-76602000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:76575000-76586000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr15:76575800-76585200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr15:76575800-76585200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:76576000-76585200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:76576000-76585600	Weak transcription	HUVEC	blood vessel
37	chr15:76576000-76585800	Weak transcription	Brain Hippocampus Middle	brain
38	chr15:76576200-76602800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:76576400-76586200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:76576600-76585800	Weak transcription	NH-A	brain
41	chr15:76577400-76585400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:76578600-76582000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:76579000-76586000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr15:76579200-76581800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:76579200-76582000	Weak transcription	Primary B cells from cord blood	blood
46	chr15:76579200-76583000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr15:76579200-76584400	Weak transcription	A549	lung
48	chr15:76579200-76585600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:76579200-76586000	Weak transcription	Brain Substantia Nigra	brain
50	chr15:76579200-76586200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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