Variant report

Variant	rs3132538
Chromosome Location	chr6:31113842-31113843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31107022..31110169-chr6:31112293..31115408,4	K562	blood:
2	chr6:31112475..31116177-chr6:31122128..31126125,5	K562	blood:
3	chr6:31107129..31110169-chr6:31111741..31115408,4	K562	blood:

Variant related genes	Relation type
ENSG00000204536	Chromatin interaction
ENSG00000204538	Chromatin interaction
ENSG00000238211	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2073722	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2233942	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2240062	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2240065	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3094227	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3094606	0.83[ASN][1000 genomes]
rs3094607	0.86[ASN][1000 genomes]
rs3094608	0.87[ASN][1000 genomes]
rs3094609	0.90[ASN][1000 genomes]
rs3094610	0.86[ASN][1000 genomes]
rs3095237	0.90[ASN][1000 genomes]
rs3095238	0.90[ASN][1000 genomes]
rs3130460	0.90[ASN][1000 genomes]
rs3130461	0.87[ASN][1000 genomes]
rs3130462	0.87[ASN][1000 genomes]
rs3130463	0.87[ASN][1000 genomes]
rs3130466	0.83[ASN][1000 genomes]
rs3130503	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3130512	0.85[ASN][1000 genomes]
rs3130952	0.85[ASN][1000 genomes]
rs3131011	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3131017	0.91[ASN][1000 genomes]
rs3132501	0.83[ASN][1000 genomes]
rs3132503	0.84[ASN][1000 genomes]
rs3132504	0.85[ASN][1000 genomes]
rs3132507	0.84[ASN][1000 genomes]
rs3132509	0.85[ASN][1000 genomes]
rs3132517	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3132539	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3132540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134789	0.88[ASN][1000 genomes]
rs4343960	0.90[ASN][1000 genomes]
rs9263761	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9263788	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
14	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
15	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
16	nsv524061	chr6:31107087-31133943	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3132538	HCG22	cis	Lymphoblastoid	GTEx
rs3132538	ZKSCAN4	cis	parietal	SCAN
rs3132538	HLA-DRB5	cis	parietal	SCAN
rs3132538	HCG22	cis	lymphoblastoid	seeQTL
rs3132538	HLA-DRB5	cis	cerebellum	SCAN
rs3132538	MLN	cis	cerebellum	SCAN
rs3132538	ANKS1A	cis	cerebellum	SCAN
rs3132538	HLA-C	cis	lymphoblastoid	GTEx
rs3132538	HLA-C///LOC732037	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31105600-31124400	Weak transcription	Fetal Kidney	kidney
2	chr6:31105600-31124800	Weak transcription	Small Intestine	intestine
3	chr6:31105800-31117000	Weak transcription	Brain Substantia Nigra	brain
4	chr6:31105800-31117200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:31105800-31117800	Weak transcription	Primary B cells from cord blood	blood
6	chr6:31105800-31121800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr6:31105800-31122600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:31105800-31124400	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:31105800-31124800	Weak transcription	Hela-S3	cervix
10	chr6:31105800-31125200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:31106000-31125000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:31106000-31125000	Weak transcription	Fetal Brain Male	brain
13	chr6:31106000-31125200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:31107600-31125000	Weak transcription	NHDF-Ad	bronchial
15	chr6:31107800-31117200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:31107800-31125000	Weak transcription	Fetal Heart	heart
17	chr6:31108000-31116200	Weak transcription	Esophagus	oesophagus
18	chr6:31109800-31114400	Strong transcription	Brain Germinal Matrix	brain
19	chr6:31109800-31114800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:31110000-31124600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:31110200-31114000	Strong transcription	Fetal Thymus	thymus
22	chr6:31110200-31114200	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr6:31110200-31114200	Strong transcription	Brain Hippocampus Middle	brain
24	chr6:31110200-31114600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:31110200-31114600	Strong transcription	Brain Anterior Caudate	brain
26	chr6:31110200-31114800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:31110200-31117200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:31110200-31125000	Weak transcription	A549	lung
29	chr6:31110400-31114000	Strong transcription	Primary T cells from cord blood	blood
30	chr6:31110400-31114800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:31110600-31117800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr6:31110800-31117000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:31110800-31117800	Weak transcription	HepG2	liver
34	chr6:31111000-31114800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:31111000-31116000	Weak transcription	Brain Angular Gyrus	brain
36	chr6:31111000-31116200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:31111000-31118800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:31111000-31121800	Weak transcription	K562	blood
39	chr6:31111000-31124400	Weak transcription	Psoas Muscle	Psoas
40	chr6:31111000-31125000	Weak transcription	NHEK	skin
41	chr6:31111000-31125200	Weak transcription	HSMMtube	muscle
42	chr6:31111200-31114000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr6:31111200-31114600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:31111200-31125000	Weak transcription	HUVEC	blood vessel
45	chr6:31111400-31114600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:31111400-31116000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr6:31111400-31117200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:31111400-31117600	Weak transcription	HSMM	muscle
49	chr6:31111400-31119600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:31111400-31124400	Strong transcription	HUES48 Cell Line	embryonic stem cell

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