Variant report

Variant	rs7547892
Chromosome Location	chr1:84658591-84658592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1021490	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1057738	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10782824	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10874427	0.87[JPT][hapmap]
rs10874428	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10874431	0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10874432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11163898	0.82[MEX][hapmap]
rs11163903	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11163905	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11163906	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.99[ASN][1000 genomes]
rs11163907	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11163908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11163911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163913	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12057561	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12064926	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12094426	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12118723	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128892	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12132002	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs12132212	0.82[ASN][1000 genomes]
rs12562031	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565896	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12723299	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12748859	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750691	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12756529	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12759624	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12760594	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1402694	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1472243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1521518	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1565823	0.90[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1874070	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037454	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037455	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2134646	0.86[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2134647	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]
rs2134648	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2134649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2174186	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2250806	0.91[JPT][hapmap]
rs2792975	0.81[JPT][hapmap]
rs3768258	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4907194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs594631	0.83[JPT][hapmap]
rs6576960	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6576961	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6576962	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576963	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658591	0.85[ASN][1000 genomes]
rs6661492	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696125	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699600	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6701486	0.91[JPT][hapmap]
rs7512288	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7515264	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7515976	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7532712	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs903263	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs955492	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970318	0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv871731	chr1:84597396-84658591	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	nsv997601	chr1:84609346-84672859	Enhancers Weak transcription ZNF genes & repeats Strong transcription 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
5	nsv1005225	chr1:84609871-84667950	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv999772	chr1:84611207-84667218	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1013911	chr1:84619164-84667950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	nsv1011105	chr1:84638386-84674276	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv1837139	chr1:84649799-84670584	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7547892	PRKACB	cis	lymphoblastoid	seeQTL
rs7547892	BCL10	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84640000-84658800	Weak transcription	Fetal Brain Male	brain
2	chr1:84640200-84658600	Weak transcription	Osteobl	bone
3	chr1:84640400-84665000	Weak transcription	NH-A	brain
4	chr1:84641200-84658600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:84644400-84658800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:84646400-84662600	Weak transcription	Colonic Mucosa	Colon
7	chr1:84647400-84658800	Strong transcription	Fetal Thymus	thymus
8	chr1:84649400-84659800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:84650000-84658800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:84650600-84658600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:84650600-84662400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:84650800-84658600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:84652200-84658600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:84652200-84675000	Weak transcription	Pancreas	Pancrea
15	chr1:84652400-84689800	Weak transcription	Aorta	Aorta
16	chr1:84652600-84658600	Weak transcription	Fetal Stomach	stomach
17	chr1:84653400-84674800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:84654000-84659400	ZNF genes & repeats	Dnd41	blood
19	chr1:84654400-84659400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
20	chr1:84654800-84658600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:84654800-84659400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
22	chr1:84654800-84660200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr1:84654800-84661000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:84654800-84661200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:84655000-84659400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
26	chr1:84655000-84661200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
27	chr1:84655200-84659600	ZNF genes & repeats	Primary B cells from cord blood	blood
28	chr1:84655200-84659600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr1:84655800-84658600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:84655800-84658600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:84655800-84660400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
32	chr1:84656200-84659600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
33	chr1:84656400-84659000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:84656400-84659000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr1:84656400-84659200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
36	chr1:84656400-84659400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
37	chr1:84656400-84659400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
38	chr1:84656400-84659600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:84656400-84660000	ZNF genes & repeats	Primary T cells from cord blood	blood
40	chr1:84656600-84659000	Strong transcription	Rectal Smooth Muscle	rectum
41	chr1:84656600-84660600	Strong transcription	Brain Cingulate Gyrus	brain
42	chr1:84656800-84659600	ZNF genes & repeats	Fetal Muscle Leg	muscle
43	chr1:84656800-84660600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
44	chr1:84657000-84658600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:84657000-84659600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:84657200-84659400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:84657200-84660400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:84657200-84665400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:84657400-84658600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:84657400-84658600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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