Variant report

Variant	rs316630
Chromosome Location	chr1:84711771-84711772
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1085727	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1085739	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11163923	0.82[JPT][hapmap]
rs11163930	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12411158	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1402695	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1402696	0.81[EUR][1000 genomes]
rs1402697	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494312	0.80[EUR][1000 genomes]
rs316628	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs4907047	0.81[EUR][1000 genomes]
rs4907050	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs588518	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs589918	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs634904	0.92[ASN][1000 genomes]
rs655977	0.81[EUR][1000 genomes]
rs657321	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674494	0.81[EUR][1000 genomes]
rs677124	0.90[ASN][1000 genomes]
rs787858	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871538	chr1:84633116-84717983	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv1816427	chr1:84670816-84715634	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv1823244	chr1:84670816-84715634	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv1824568	chr1:84670816-84715634	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv1822734	chr1:84678418-84715634	ZNF genes & repeats Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	esv1845114	chr1:84678418-84715634	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	esv1851921	chr1:84678418-84715634	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	esv1824421	chr1:84704329-84719245	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	esv2527540	chr1:84710029-84716624	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3319327	chr1:84710064-84717462	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv3500348	chr1:84710764-84717162	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1810416	chr1:84710840-84715634	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1812140	chr1:84710840-84715634	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv1844994	chr1:84710840-84715634	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv1847249	chr1:84710840-84715634	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv1813109	chr1:84710840-84717983	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	esv1843502	chr1:84710840-84717983	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv436488	chr1:84711229-84715993	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv3500353	chr1:84711314-84717012	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	esv3319331	chr1:84711389-84716737	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	esv2607567	chr1:84711412-84716583	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	esv20356	chr1:84711621-84715809	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	esv5501	chr1:84711762-84716093	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv546691	chr1:84711771-84715634	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs316630	PRKACB	cis	lymphoblastoid	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84675200-84712800	Weak transcription	NH-A	brain
2	chr1:84685600-84713400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:84690000-84719400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:84690400-84711800	Weak transcription	Spleen	Spleen
5	chr1:84691200-84712200	Weak transcription	Pancreas	Pancrea
6	chr1:84699600-84713000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:84701200-84711800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:84701200-84713200	Weak transcription	Colonic Mucosa	Colon
9	chr1:84701200-84717400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:84701200-84718400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:84701200-84719600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:84701400-84713000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:84701400-84713000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:84701400-84719800	Weak transcription	Fetal Heart	heart
15	chr1:84701400-84719800	Weak transcription	HSMM	muscle
16	chr1:84702800-84713200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:84705800-84711800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:84705800-84712000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:84705800-84713000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:84705800-84723000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:84706000-84711800	Weak transcription	Brain Anterior Caudate	brain
22	chr1:84706000-84711800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:84706000-84713000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:84706000-84713400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:84706200-84711800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:84706200-84713400	Weak transcription	Fetal Intestine Large	intestine
27	chr1:84706600-84713000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:84710600-84711800	Enhancers	HUVEC	blood vessel
29	chr1:84711000-84712800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:84711000-84713800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:84711200-84712400	Enhancers	Brain Substantia Nigra	brain
32	chr1:84711200-84712400	Enhancers	Stomach Mucosa	stomach
33	chr1:84711200-84713000	Enhancers	K562	blood
34	chr1:84711400-84711800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:84711600-84711800	Enhancers	Brain Hippocampus Middle	brain
36	chr1:84711600-84711800	Enhancers	Fetal Lung	lung
37	chr1:84711600-84712200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr1:84711600-84712400	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr1:84711600-84712400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:84711600-84712400	Enhancers	HepG2	liver
41	chr1:84711600-84712600	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr1:84711600-84713000	Enhancers	A549	lung
43	chr1:84711600-84713200	Enhancers	Rectal Mucosa Donor 31	rectum

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