Variant report

Variant	rs458967
Chromosome Location	chr5:112170358-112170359
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	chr5:112163610..112167333-chr5:112168382..112170842,3	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10463643	0.81[EUR][1000 genomes]
rs1441375	0.85[EUR][1000 genomes]
rs1661035	0.87[EUR][1000 genomes]
rs1661036	0.87[EUR][1000 genomes]
rs1734243	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs187075	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1966476	0.86[EUR][1000 genomes]
rs1966477	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2229992	0.84[EUR][1000 genomes]
rs2439591	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2464805	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2545159	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2545162	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2545163	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2545164	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2545165	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2545169	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2546110	0.84[EUR][1000 genomes]
rs2546111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2546116	0.88[EUR][1000 genomes]
rs2952615	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs351771	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs386830	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs392907	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs395266	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs397768	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs401908	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41115	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs411356	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs42427	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs433429	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs434157	0.85[ASN][1000 genomes]
rs459552	0.93[ASN][1000 genomes]
rs464002	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs464708	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs465899	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs468179	0.88[EUR][1000 genomes]
rs501250	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs529076	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs544243	0.93[ASN][1000 genomes]
rs563556	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs866006	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv1034239	chr5:112161239-112194693	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs458967	SRP19	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
4	chr5:112132000-112174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:112136600-112176200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:112149400-112176400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:112150200-112177800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:112151400-112176400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr5:112152000-112170400	Weak transcription	Brain Angular Gyrus	brain
12	chr5:112152000-112183800	Weak transcription	Gastric	stomach
13	chr5:112152200-112172000	Weak transcription	NHLF	lung
14	chr5:112153200-112179400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:112153200-112179800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:112154000-112175200	Weak transcription	Stomach Mucosa	stomach
17	chr5:112154400-112179400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:112154600-112177800	Strong transcription	Primary T cells from cord blood	blood
19	chr5:112155000-112183800	Weak transcription	Aorta	Aorta
20	chr5:112155200-112173600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:112155800-112173400	Weak transcription	Pancreas	Pancrea
22	chr5:112155800-112173800	Weak transcription	Hela-S3	cervix
23	chr5:112156000-112173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:112156000-112173400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:112156000-112173400	Weak transcription	Fetal Heart	heart
26	chr5:112156200-112179000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:112158600-112173200	Weak transcription	Fetal Kidney	kidney
28	chr5:112158800-112173400	Weak transcription	Fetal Brain Male	brain
29	chr5:112160600-112176200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:112162000-112172800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr5:112162000-112175200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:112162400-112171000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:112162600-112174600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:112162800-112171400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:112163400-112171600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:112163400-112183800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:112163600-112172000	Weak transcription	NH-A	brain
38	chr5:112164000-112175200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr5:112164200-112172600	Weak transcription	A549	lung
40	chr5:112164200-112173200	Weak transcription	NHEK	skin
41	chr5:112164200-112173400	Weak transcription	HUVEC	blood vessel
42	chr5:112164400-112173400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr5:112164600-112173200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr5:112165000-112172800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:112165200-112173400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr5:112165400-112172600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr5:112165400-112173200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr5:112165400-112173200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:112165400-112182400	Weak transcription	Right Ventricle	heart
50	chr5:112165600-112170800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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