Variant report

Variant	rs2134647
Chromosome Location	chr1:84678418-84678419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1021490	0.96[CEU][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10493750	0.83[MEX][hapmap]
rs1057738	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10782824	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10874428	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10874431	0.92[CEU][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10874432	1.00[CEU][hapmap];0.84[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11163898	0.87[MEX][hapmap]
rs11163900	0.83[MEX][hapmap]
rs11163903	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11163905	0.96[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11163906	0.96[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11163907	0.96[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11163908	0.96[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11163911	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11163913	0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12057561	0.92[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12064926	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12094426	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12118723	1.00[CEU][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12128892	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12132002	0.81[JPT][hapmap]
rs12132212	0.87[EUR][1000 genomes]
rs12404263	0.83[MEX][hapmap]
rs12405120	0.84[GIH][hapmap]
rs12562031	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12565896	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12723299	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12748859	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12750691	0.96[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12756529	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12759624	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12760594	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1402694	0.96[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1472243	0.96[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1521518	0.88[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1565823	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1874070	0.96[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2037454	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2037455	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2134646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134648	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2134649	1.00[CEU][hapmap];0.85[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2174186	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768258	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4907194	1.00[CEU][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs594631	0.88[JPT][hapmap]
rs6576960	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6576961	0.96[CEU][hapmap];0.84[JPT][hapmap]
rs6576962	0.96[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6576963	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6658591	0.82[EUR][1000 genomes]
rs6661492	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6695305	0.96[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6695851	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6696125	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6699600	0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7512288	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7515264	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7515976	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7532712	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7547892	0.93[ASW][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs903263	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs953197	0.81[GIH][hapmap]
rs955492	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs970318	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871656	chr1:84601048-84693671	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv871375	chr1:84622793-84678418	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv871643	chr1:84628655-84705481	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2134647	PRKACB	cis	lymphoblastoid	seeQTL
rs2134647	BCL10	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84652400-84689800	Weak transcription	Aorta	Aorta
2	chr1:84657600-84708000	Weak transcription	Left Ventricle	heart
3	chr1:84659000-84685000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:84659000-84700600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:84659000-84700800	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:84659200-84688400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:84659400-84685400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:84659800-84701400	Weak transcription	NHLF	lung
9	chr1:84660600-84683200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:84660600-84686200	Weak transcription	Fetal Intestine Small	intestine
11	chr1:84660800-84688400	Weak transcription	Fetal Brain Male	brain
12	chr1:84663200-84684600	Weak transcription	Hela-S3	cervix
13	chr1:84665200-84700800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:84665400-84684000	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:84665400-84684600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:84665400-84685200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:84665400-84687600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:84665400-84700600	Weak transcription	Colonic Mucosa	Colon
19	chr1:84665400-84701000	Weak transcription	Fetal Kidney	kidney
20	chr1:84665600-84684800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:84665800-84680200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:84665800-84681800	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:84665800-84684400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:84666000-84679600	Weak transcription	Thymus	Thymus
25	chr1:84666000-84689800	Weak transcription	Fetal Stomach	stomach
26	chr1:84666200-84682600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:84666200-84683800	Weak transcription	Fetal Lung	lung
28	chr1:84666800-84710200	Weak transcription	HSMMtube	muscle
29	chr1:84667600-84680600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:84668200-84690000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:84669800-84683000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:84670200-84682600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:84670800-84683400	Weak transcription	Esophagus	oesophagus
34	chr1:84672400-84683800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:84672400-84684200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:84672600-84679800	Weak transcription	Adipose Nuclei	Adipose
37	chr1:84672600-84683000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:84672600-84683000	Weak transcription	Ovary	ovary
39	chr1:84672600-84683200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:84672600-84683400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:84672600-84685200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:84672600-84685200	Weak transcription	Fetal Intestine Large	intestine
43	chr1:84672600-84687400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:84672600-84689800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:84672600-84700600	Weak transcription	Brain Anterior Caudate	brain
46	chr1:84672600-84701000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:84672600-84711200	Weak transcription	Brain Substantia Nigra	brain
48	chr1:84672800-84684200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:84672800-84685000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:84673000-84680400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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