Variant report

Variant	rs2415524
Chromosome Location	chr14:39514763-39514764
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	chr14:39513894..39516551-chr14:39652021..39654125,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10140341	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10141471	0.90[ASN][1000 genomes]
rs11157041	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12164875	0.80[EUR][1000 genomes]
rs12879229	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12883061	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12885242	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12894046	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1555257	0.92[ASN][1000 genomes]
rs17108728	0.90[ASN][1000 genomes]
rs28502115	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28699217	0.92[ASN][1000 genomes]
rs28810420	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34642409	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34676226	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34985331	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35224434	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35423721	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35992529	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36161173	0.94[ASN][1000 genomes]
rs3742354	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742355	0.95[ASN][1000 genomes]
rs3759545	0.83[AMR][1000 genomes]
rs4902308	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902406	0.81[AMR][1000 genomes]
rs6571893	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71407775	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7152746	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7153124	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9322992	0.84[EUR][1000 genomes];0.95[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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2415524	SIP1	Cis_1M	lymphoblastoid	RTeQTL
rs2415524	TRAPPC6B	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39495400-39518200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:39495800-39516000	Weak transcription	Stomach Mucosa	stomach
3	chr14:39496000-39514800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr14:39496000-39520400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr14:39497400-39518000	Strong transcription	HSMM	muscle
6	chr14:39497400-39519200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr14:39497800-39520400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr14:39497800-39521200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr14:39498000-39518400	Strong transcription	Osteobl	bone
10	chr14:39498000-39518600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr14:39498000-39524200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr14:39498200-39519400	Strong transcription	NH-A	brain
13	chr14:39498200-39524200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr14:39498200-39524400	Strong transcription	Fetal Intestine Large	intestine
15	chr14:39498400-39520000	Strong transcription	HepG2	liver
16	chr14:39498400-39524800	Weak transcription	K562	blood
17	chr14:39498600-39518000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr14:39498600-39519600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr14:39498600-39524000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr14:39498600-39524800	Strong transcription	Adipose Nuclei	Adipose
21	chr14:39499000-39523200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr14:39499000-39523600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr14:39499000-39524200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr14:39499000-39524800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr14:39499000-39524800	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr14:39499000-39525000	Strong transcription	Liver	Liver
27	chr14:39499600-39524600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr14:39500000-39519800	Weak transcription	Pancreas	Pancrea
29	chr14:39500000-39521000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr14:39500000-39522800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr14:39500000-39524400	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr14:39500000-39524800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr14:39500000-39525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr14:39500200-39515200	Weak transcription	Lung	lung
35	chr14:39500200-39515800	Weak transcription	Esophagus	oesophagus
36	chr14:39500200-39518600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr14:39500200-39519400	Weak transcription	Gastric	stomach
38	chr14:39500200-39523000	Weak transcription	Spleen	Spleen
39	chr14:39500400-39519800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr14:39501400-39524800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr14:39502000-39518400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr14:39502600-39524200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr14:39504000-39519200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr14:39504000-39519600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr14:39504000-39519800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr14:39504200-39524000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr14:39504600-39517800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr14:39504800-39519400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr14:39504800-39523000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr14:39505000-39517800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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