Variant report

Variant	rs12066159
Chromosome Location	chr1:92204798-92204799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92198152..92200213-chr1:92201193..92206399,7	K562	blood:
2	chr1:92196960..92199922-chr1:92201744..92205146,4	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10874909	0.81[CHD][hapmap]
rs11165377	0.95[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs11165390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165410	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11801868	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12061269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12067583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076549	0.95[CHB][hapmap];0.91[CHD][hapmap]
rs12123737	0.81[ASN][1000 genomes]
rs17131541	0.81[CHD][hapmap]
rs17513917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029356	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs284876	0.84[CHB][hapmap]
rs4658112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats 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	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
7	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12066159	RPAP2	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92197000-92215200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:92197200-92215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:92197600-92230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:92197800-92211000	Weak transcription	Colonic Mucosa	Colon
5	chr1:92198000-92210400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:92198200-92206600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:92198200-92224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:92198400-92207000	Weak transcription	Gastric	stomach
9	chr1:92198400-92207400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:92198400-92210400	Weak transcription	HUVEC	blood vessel
11	chr1:92198600-92207600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:92199000-92206200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:92199200-92218600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:92199400-92219000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:92200600-92205000	Genic enhancers	HepG2	liver
16	chr1:92201000-92205200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:92201000-92208600	Weak transcription	Small Intestine	intestine
18	chr1:92201200-92219000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:92201400-92217600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:92202200-92204800	Genic enhancers	Placenta	Placenta
21	chr1:92202400-92205400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr1:92203000-92204800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:92203000-92206800	Weak transcription	Pancreas	Pancrea
24	chr1:92203000-92208200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:92203000-92208400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:92203000-92208600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:92203000-92210400	Weak transcription	Brain Angular Gyrus	brain
28	chr1:92203200-92205000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:92203200-92206600	Weak transcription	K562	blood
30	chr1:92203200-92207200	Weak transcription	Right Atrium	heart
31	chr1:92203200-92207400	Weak transcription	Esophagus	oesophagus
32	chr1:92203200-92207600	Weak transcription	Aorta	Aorta
33	chr1:92203200-92207600	Weak transcription	Psoas Muscle	Psoas
34	chr1:92203200-92207600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:92203200-92208600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:92203200-92210200	Weak transcription	Brain Anterior Caudate	brain
37	chr1:92203200-92210400	Weak transcription	Stomach Mucosa	stomach
38	chr1:92203200-92212800	Weak transcription	Spleen	Spleen
39	chr1:92203400-92204800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:92203400-92205000	Strong transcription	Adipose Nuclei	Adipose
41	chr1:92203400-92205000	Strong transcription	Fetal Muscle Trunk	muscle
42	chr1:92203400-92205200	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:92203400-92205400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:92203400-92206400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:92203400-92206400	Weak transcription	NH-A	brain
46	chr1:92203400-92206400	Weak transcription	Osteobl	bone
47	chr1:92203400-92206600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:92203400-92206600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:92203400-92206600	Weak transcription	Left Ventricle	heart
50	chr1:92203400-92206800	Weak transcription	Rectal Smooth Muscle	rectum

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