Variant report

Variant	rs6571893
Chromosome Location	chr14:39538085-39538086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10136536	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10140341	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10141471	0.90[ASN][1000 genomes]
rs11157041	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12164875	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12879229	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12883061	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12885242	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12894046	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1555257	0.91[ASN][1000 genomes]
rs17108728	0.90[ASN][1000 genomes]
rs2415524	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28485301	0.80[AMR][1000 genomes]
rs28502115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28699217	0.94[ASN][1000 genomes]
rs28810420	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34642409	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34676226	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34816815	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34985331	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35035794	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35224434	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35423721	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35992529	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36161173	0.93[ASN][1000 genomes]
rs3742354	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742355	0.94[ASN][1000 genomes]
rs3759545	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4902308	0.94[ASN][1000 genomes]
rs4902405	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4902406	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6571892	0.86[AFR][1000 genomes]
rs71407775	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7152746	0.94[ASN][1000 genomes]
rs7153124	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73285796	0.86[AFR][1000 genomes]
rs8012820	0.86[AFR][1000 genomes]
rs9322992	0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6571893	SIP1	Cis_1M	lymphoblastoid	RTeQTL
rs6571893	TRAPPC6B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39523800-39540200	Weak transcription	Psoas Muscle	Psoas
2	chr14:39525400-39540600	Strong transcription	NH-A	brain
3	chr14:39525600-39540600	Strong transcription	HSMM	muscle
4	chr14:39525600-39541000	Weak transcription	Brain Angular Gyrus	brain
5	chr14:39525600-39565600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr14:39526000-39557200	Strong transcription	Osteobl	bone
7	chr14:39526400-39563200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr14:39526800-39538400	Strong transcription	Liver	Liver
9	chr14:39526800-39540400	Weak transcription	Spleen	Spleen
10	chr14:39526800-39540800	Weak transcription	Right Ventricle	heart
11	chr14:39526800-39541200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr14:39526800-39552600	Weak transcription	Gastric	stomach
13	chr14:39526800-39553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr14:39526800-39554000	Weak transcription	Aorta	Aorta
15	chr14:39526800-39554000	Weak transcription	Esophagus	oesophagus
16	chr14:39526800-39554200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr14:39526800-39554200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr14:39526800-39566600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr14:39527000-39539000	Weak transcription	Lung	lung
20	chr14:39527000-39540600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr14:39527000-39540600	Weak transcription	Thymus	Thymus
22	chr14:39527000-39541800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr14:39527000-39554200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:39527000-39565400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr14:39527400-39538200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr14:39527400-39538400	Strong transcription	HepG2	liver
27	chr14:39527400-39549000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr14:39527600-39554200	Weak transcription	K562	blood
29	chr14:39528000-39547800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr14:39528000-39565400	Strong transcription	Placenta	Placenta
31	chr14:39528000-39565600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr14:39528200-39545800	Strong transcription	Dnd41	blood
33	chr14:39528200-39548800	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr14:39528600-39566400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr14:39529200-39559400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr14:39529200-39566600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr14:39529600-39539400	Weak transcription	HMEC	breast
38	chr14:39529600-39539800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr14:39529600-39564200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr14:39529800-39554200	Weak transcription	Fetal Brain Male	brain
41	chr14:39529800-39566400	Weak transcription	Fetal Heart	heart
42	chr14:39530200-39540200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr14:39530600-39552000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr14:39531000-39539000	Weak transcription	Brain Anterior Caudate	brain
45	chr14:39531200-39540800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr14:39531200-39541600	Weak transcription	Brain Substantia Nigra	brain
47	chr14:39531200-39569200	Weak transcription	Stomach Mucosa	stomach
48	chr14:39531400-39545800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr14:39531600-39543000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr14:39532000-39565400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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