Variant report

Variant	rs533134
Chromosome Location	chr1:227290139-227290140
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10458379	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916098	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10916117	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12035190	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12035998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12038272	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs12080452	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12095674	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12097121	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1929859	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104863	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2458523	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482453	1.00[ASN][1000 genomes]
rs2777833	0.88[JPT][hapmap]
rs2777841	0.84[JPT][hapmap]
rs2997438	0.86[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs4551562	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653477	0.82[ASN][1000 genomes]
rs4653788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482032	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs567467	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58442036	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs595155	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61834563	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61834564	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61836477	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs645081	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664803	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688718	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536444	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs871210	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv3405731	chr1:227288729-227293227	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	inside rSNPs	n/a
11	esv3444191	chr1:227289529-227293427	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	n/a
12	esv3381954	chr1:227290079-227293277	Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	n/a
13	nsv522990	chr1:227290139-227302912	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv549270	chr1:227290139-227361072	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs533134	PARP1	cis	cerebellum	SCAN
rs533134	MIXL1	cis	parietal	SCAN
rs533134	TRIM17	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
4	chr1:227247400-227299800	Weak transcription	HMEC	breast
5	chr1:227251000-227300000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:227257800-227312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
8	chr1:227271800-227299600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:227272600-227294400	Weak transcription	Fetal Heart	heart
10	chr1:227272800-227295000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:227272800-227295000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:227272800-227331000	Weak transcription	Lung	lung
13	chr1:227273000-227312400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:227275800-227302600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:227277200-227302600	Weak transcription	Brain Substantia Nigra	brain
16	chr1:227279800-227299000	Weak transcription	Placenta	Placenta
17	chr1:227280800-227298800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:227281800-227294400	Weak transcription	Fetal Kidney	kidney
19	chr1:227282600-227318000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:227285600-227297600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:227285600-227308600	Weak transcription	Pancreas	Pancrea
22	chr1:227285600-227313800	Weak transcription	Gastric	stomach
23	chr1:227286200-227290200	Strong transcription	HUVEC	blood vessel
24	chr1:227286400-227328200	Weak transcription	Brain Germinal Matrix	brain
25	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
26	chr1:227288000-227294000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:227288000-227326400	Weak transcription	A549	lung
28	chr1:227288200-227294600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:227288200-227296400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:227288200-227332400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:227288400-227294600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:227288400-227297600	Weak transcription	NH-A	brain
33	chr1:227288400-227299400	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:227288400-227299400	Weak transcription	Ovary	ovary
35	chr1:227288400-227299600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:227288400-227299600	Weak transcription	Osteobl	bone
37	chr1:227288400-227302200	Weak transcription	Fetal Brain Male	brain
38	chr1:227288400-227343000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:227288600-227293400	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:227288600-227294200	Weak transcription	Fetal Brain Female	brain
42	chr1:227288600-227294400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:227288600-227294400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:227288600-227294600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:227288600-227294600	Weak transcription	Brain Angular Gyrus	brain
46	chr1:227288600-227294600	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:227288600-227294600	Weak transcription	Fetal Lung	lung
48	chr1:227288600-227294800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:227288600-227294800	Weak transcription	HSMMtube	muscle
50	chr1:227288600-227295000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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