Variant report

Variant	rs28810420
Chromosome Location	chr14:39540983-39540984
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10136536	0.83[EUR][1000 genomes]
rs10140341	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10141471	0.90[ASN][1000 genomes]
rs11157041	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12164875	0.82[EUR][1000 genomes]
rs12879229	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12883061	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12885242	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12894046	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1555257	0.91[ASN][1000 genomes]
rs17108728	0.90[ASN][1000 genomes]
rs2415524	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28502115	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28699217	0.94[ASN][1000 genomes]
rs34642409	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34676226	0.94[ASN][1000 genomes]
rs34816815	0.81[EUR][1000 genomes]
rs34985331	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35035794	0.83[EUR][1000 genomes]
rs35224434	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35423721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35992529	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36161173	0.93[ASN][1000 genomes]
rs3742354	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742355	0.94[ASN][1000 genomes]
rs3759545	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4902308	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902405	0.81[EUR][1000 genomes]
rs4902406	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6571892	0.86[AFR][1000 genomes]
rs6571893	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71407775	0.94[ASN][1000 genomes]
rs7152746	0.94[ASN][1000 genomes]
rs7153124	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73285796	0.86[AFR][1000 genomes]
rs8012820	0.86[AFR][1000 genomes]
rs9322992	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28810420	SIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39525600-39541000	Weak transcription	Brain Angular Gyrus	brain
2	chr14:39525600-39565600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr14:39526000-39557200	Strong transcription	Osteobl	bone
4	chr14:39526400-39563200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr14:39526800-39541200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr14:39526800-39552600	Weak transcription	Gastric	stomach
7	chr14:39526800-39553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr14:39526800-39554000	Weak transcription	Aorta	Aorta
9	chr14:39526800-39554000	Weak transcription	Esophagus	oesophagus
10	chr14:39526800-39554200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr14:39526800-39554200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:39526800-39566600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:39527000-39541800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr14:39527000-39554200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:39527000-39565400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr14:39527400-39549000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr14:39527600-39554200	Weak transcription	K562	blood
18	chr14:39528000-39547800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr14:39528000-39565400	Strong transcription	Placenta	Placenta
20	chr14:39528000-39565600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr14:39528200-39545800	Strong transcription	Dnd41	blood
22	chr14:39528200-39548800	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr14:39528600-39566400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:39529200-39559400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr14:39529200-39566600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr14:39529600-39564200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr14:39529800-39554200	Weak transcription	Fetal Brain Male	brain
28	chr14:39529800-39566400	Weak transcription	Fetal Heart	heart
29	chr14:39530600-39552000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr14:39531200-39541600	Weak transcription	Brain Substantia Nigra	brain
31	chr14:39531200-39569200	Weak transcription	Stomach Mucosa	stomach
32	chr14:39531400-39545800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr14:39531600-39543000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr14:39532000-39565400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr14:39534000-39543200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr14:39534200-39541400	Weak transcription	Fetal Brain Female	brain
37	chr14:39534200-39545800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr14:39534200-39566600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr14:39534600-39541600	Weak transcription	NHEK	skin
40	chr14:39534600-39554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr14:39534600-39566800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr14:39534800-39541200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr14:39534800-39541600	Weak transcription	Fetal Kidney	kidney
44	chr14:39534800-39541800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr14:39534800-39547600	Weak transcription	Hela-S3	cervix
46	chr14:39534800-39553600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr14:39535000-39550000	Weak transcription	NHLF	lung
48	chr14:39535400-39553600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr14:39536000-39541800	Weak transcription	Fetal Lung	lung
50	chr14:39536000-39543000	Weak transcription	Colonic Mucosa	Colon

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