Variant report

Variant	rs4340100
Chromosome Location	chr12:20775707-20775708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10770677	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10841575	0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs11045330	0.89[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11045331	0.81[CEU][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11045332	1.00[YRI][hapmap]
rs11045336	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11045337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045338	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045344	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12312310	1.00[YRI][hapmap]
rs12578604	0.98[ASN][1000 genomes]
rs12578606	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12581101	0.81[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs35380579	0.96[ASN][1000 genomes]
rs4309199	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4315134	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4359258	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4375483	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4393371	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4397903	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4499055	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4533093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73080758	0.98[ASN][1000 genomes]
rs73080759	0.95[ASN][1000 genomes]
rs73080764	0.98[ASN][1000 genomes]
rs73080767	0.96[ASN][1000 genomes]
rs7968002	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7977337	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.96[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	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1054997	chr12:20682009-21292602	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv557702	chr12:20755626-20779078	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
7	nsv469158	chr12:20766559-20783761	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
8	nsv557703	chr12:20766559-20783761	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4340100	PYROXD1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20756200-20780200	Weak transcription	Fetal Stomach	stomach
2	chr12:20756200-20784400	Weak transcription	Fetal Muscle Leg	muscle
3	chr12:20761400-20781400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:20761400-20784200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:20763000-20780200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:20765200-20781400	Weak transcription	HUVEC	blood vessel
7	chr12:20765800-20782000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:20766600-20780400	Weak transcription	Aorta	Aorta
9	chr12:20766600-20787800	Weak transcription	Right Ventricle	heart
10	chr12:20766600-20805000	Strong transcription	Hela-S3	cervix
11	chr12:20767600-20781800	Weak transcription	Ovary	ovary
12	chr12:20767600-20787800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:20767800-20782800	Weak transcription	Fetal Kidney	kidney
14	chr12:20768000-20813600	Weak transcription	Colonic Mucosa	Colon
15	chr12:20768600-20782600	Weak transcription	NH-A	brain
16	chr12:20769400-20779400	Weak transcription	Fetal Intestine Small	intestine
17	chr12:20769800-20781200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:20769800-20781200	Weak transcription	Osteobl	bone
19	chr12:20769800-20781800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:20769800-20787200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr12:20773200-20780600	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:20773400-20777800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:20773600-20779800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:20773800-20776400	Strong transcription	Fetal Intestine Large	intestine
25	chr12:20774000-20810800	Weak transcription	Placenta	Placenta
26	chr12:20775000-20775800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr12:20775400-20782600	Weak transcription	Left Ventricle	heart
28	chr12:20775600-20777400	Weak transcription	Rectal Mucosa Donor 31	rectum

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