Variant report

Variant	rs13194610
Chromosome Location	chr6:117591755-117591756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13199476	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13208901	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210974	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210975	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210976	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28391390	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35421344	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35998625	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57100713	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61153326	0.86[AFR][1000 genomes]
rs71570842	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71570843	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9387459	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9387461	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9387462	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948766	chr6:117407275-117641016	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2758076	chr6:117431224-117627275	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2759465	chr6:117431224-117627275	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830785	chr6:117448943-117627275	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2757190	chr6:117464048-117609529	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13194610	PIGC	trans	lymphoblastoid	seeQTL
rs13194610	RFX6	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117590600-117591800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr6:117590800-117592400	Active TSS	Psoas Muscle	Psoas
3	chr6:117591000-117591800	Bivalent Enhancer	Fetal Brain Male	brain
4	chr6:117591000-117592400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr6:117591000-117592400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr6:117591000-117592400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:117591000-117592400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:117591000-117592400	Bivalent Enhancer	Liver	Liver
9	chr6:117591000-117592400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
10	chr6:117591000-117592800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr6:117591000-117593400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:117591200-117591800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr6:117591200-117591800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:117591200-117591800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
15	chr6:117591200-117591800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:117591200-117591800	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
17	chr6:117591200-117591800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
18	chr6:117591200-117591800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
19	chr6:117591200-117591800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
20	chr6:117591200-117591800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
21	chr6:117591200-117591800	Bivalent Enhancer	Ovary	ovary
22	chr6:117591200-117591800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
23	chr6:117591200-117591800	Bivalent Enhancer	NHEK	skin
24	chr6:117591200-117592000	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:117591200-117592000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:117591200-117592000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
27	chr6:117591200-117592000	Bivalent/Poised TSS	A549	lung
28	chr6:117591200-117592200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
29	chr6:117591200-117592400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr6:117591200-117592400	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:117591200-117592400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:117591200-117592400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:117591200-117592400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:117591200-117592400	Enhancers	Gastric	stomach
35	chr6:117591200-117592400	Bivalent Enhancer	Lung	lung
36	chr6:117591200-117592400	Bivalent Enhancer	Spleen	Spleen
37	chr6:117591400-117591800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr6:117591400-117591800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
39	chr6:117591400-117591800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
40	chr6:117591400-117591800	Flanking Bivalent TSS/Enh	NH-A	brain
41	chr6:117591400-117592000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:117591400-117592000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:117591400-117592000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:117591400-117592000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
45	chr6:117591400-117592000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:117591400-117592000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:117591400-117592000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:117591400-117592000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:117591400-117592000	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion
50	chr6:117591400-117592000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum

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