Variant report

Variant	rs17504359
Chromosome Location	chr4:151307121-151307122
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12499470	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500337	0.89[ASN][1000 genomes]
rs12502486	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503093	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12506612	0.82[ASN][1000 genomes]
rs12507785	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12508149	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17504442	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17589028	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17589134	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1979920	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2036552	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2360071	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41386148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56714695	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535735	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6812262	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6817796	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6833359	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6839345	0.82[ASN][1000 genomes]
rs6849869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7677055	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7681051	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699001	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180280	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs952097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv880259	chr4:151210761-151367745	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv880260	chr4:151214038-151331191	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv830112	chr4:151243801-151431771	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17504359	LRBA	cis	parietal	SCAN
rs17504359	PLRG1	cis	parietal	SCAN
rs17504359	TTC29	cis	cerebellum	SCAN
rs17504359	LRBA	cis	cerebellum	SCAN
rs17504359	FAM160A1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151243000-151312000	Weak transcription	Primary B cells from cord blood	blood
2	chr4:151262400-151311200	Weak transcription	Primary T cells from cord blood	blood
3	chr4:151272000-151371400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:151286600-151355600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr4:151290200-151367400	Weak transcription	K562	blood
6	chr4:151291800-151314200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:151292400-151361000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:151293600-151307200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:151294200-151314000	Weak transcription	Fetal Intestine Small	intestine
10	chr4:151296000-151317200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:151297200-151314000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:151299800-151314600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr4:151301600-151315600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:151302400-151307200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:151304800-151307400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr4:151305000-151307400	Enhancers	Osteobl	bone
17	chr4:151305400-151307400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr4:151305400-151307400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:151305400-151307400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr4:151305400-151307600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:151305400-151307600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:151305600-151307200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr4:151306400-151307200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:151306400-151307400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr4:151306400-151307400	Enhancers	NHDF-Ad	bronchial
26	chr4:151306600-151307200	Enhancers	Colon Smooth Muscle	Colon
27	chr4:151306600-151307400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:151306600-151307400	Enhancers	NHLF	lung
29	chr4:151306600-151307800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:151306800-151307200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:151306800-151307200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:151306800-151307200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:151306800-151307200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:151306800-151307200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:151306800-151307200	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr4:151306800-151307200	Enhancers	Fetal Muscle Leg	muscle
37	chr4:151306800-151307200	Enhancers	Placenta	Placenta
38	chr4:151306800-151307200	Enhancers	Left Ventricle	heart
39	chr4:151306800-151307200	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr4:151306800-151307200	Enhancers	Right Atrium	heart
41	chr4:151306800-151307400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:151306800-151307400	Enhancers	Adipose Nuclei	Adipose
43	chr4:151306800-151307400	Enhancers	Fetal Heart	heart
44	chr4:151307000-151309400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:151307000-151348800	Weak transcription	Aorta	Aorta

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