Variant report

Variant	rs187075
Chromosome Location	chr5:112164238-112164239
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	chr5:112156563..112159936-chr5:112161937..112165418,3	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12656359	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1441375	0.83[EUR][1000 genomes]
rs1661035	0.85[EUR][1000 genomes]
rs1661036	0.85[EUR][1000 genomes]
rs1734243	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1966476	0.86[EUR][1000 genomes]
rs1966477	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2229992	0.86[EUR][1000 genomes]
rs2431240	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2439591	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2464805	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2545159	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2545162	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2545163	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2545164	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2545165	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2545169	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2546110	0.86[EUR][1000 genomes]
rs2546111	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2546116	0.88[EUR][1000 genomes]
rs2909786	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2909787	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2909958	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2952615	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351771	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs386830	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs392907	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs395266	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs397768	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs401908	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41115	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs411356	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42427	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs433429	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs458967	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs464002	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs464708	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs465899	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs468179	0.86[EUR][1000 genomes]
rs481789	0.86[ASN][1000 genomes]
rs497844	0.84[ASN][1000 genomes]
rs501250	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs529076	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs563556	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs565453	0.86[ASN][1000 genomes]
rs565603	0.84[ASN][1000 genomes]
rs569940	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs866006	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][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
rs187075	SRP19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr5:112145400-112165600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:112146200-112165800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:112149400-112176400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr5:112149800-112166400	Strong transcription	Fetal Thymus	thymus
12	chr5:112150200-112177800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:112150400-112166600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr5:112151400-112176400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr5:112152000-112170400	Weak transcription	Brain Angular Gyrus	brain
16	chr5:112152000-112183800	Weak transcription	Gastric	stomach
17	chr5:112152200-112172000	Weak transcription	NHLF	lung
18	chr5:112153200-112169600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:112153200-112179400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:112153200-112179800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:112153400-112165800	Strong transcription	Liver	Liver
22	chr5:112154000-112175200	Weak transcription	Stomach Mucosa	stomach
23	chr5:112154400-112179400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:112154600-112177800	Strong transcription	Primary T cells from cord blood	blood
25	chr5:112154800-112165600	Strong transcription	Osteobl	bone
26	chr5:112155000-112183800	Weak transcription	Aorta	Aorta
27	chr5:112155200-112173600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:112155800-112173400	Weak transcription	Pancreas	Pancrea
29	chr5:112155800-112173800	Weak transcription	Hela-S3	cervix
30	chr5:112156000-112173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:112156000-112173400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr5:112156000-112173400	Weak transcription	Fetal Heart	heart
33	chr5:112156200-112179000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:112158600-112173200	Weak transcription	Fetal Kidney	kidney
35	chr5:112158800-112173400	Weak transcription	Fetal Brain Male	brain
36	chr5:112159200-112165200	Weak transcription	GM12878-XiMat	blood
37	chr5:112159600-112165600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr5:112160600-112166800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:112160600-112176200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr5:112160800-112166000	Strong transcription	NHDF-Ad	bronchial
41	chr5:112160800-112166200	Strong transcription	Brain Substantia Nigra	brain
42	chr5:112160800-112168400	Strong transcription	Adipose Nuclei	Adipose
43	chr5:112160800-112168600	Strong transcription	Dnd41	blood
44	chr5:112160800-112168800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:112161000-112166600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr5:112161600-112165600	Weak transcription	K562	blood
47	chr5:112162000-112165600	Strong transcription	Brain Germinal Matrix	brain
48	chr5:112162000-112172800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr5:112162000-112175200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr5:112162400-112166200	Strong transcription	Primary B cells from peripheral blood	blood

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