Variant report

Variant	rs11854213
Chromosome Location	chr15:55970041-55970042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1014551	1.00[ASW][hapmap];0.83[CEU][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10518817	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10851589	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11852298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12373006	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12438177	0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12442771	0.81[CHB][hapmap]
rs12591246	0.81[CHB][hapmap]
rs12903822	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs1438918	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16976450	0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs16976466	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16976472	0.91[CHB][hapmap]
rs1814329	0.81[CHB][hapmap]
rs2008336	0.85[CHB][hapmap]
rs2118781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2414424	0.86[CHB][hapmap]
rs2414426	0.86[CHB][hapmap]
rs2414427	0.86[CHB][hapmap]
rs2414431	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs28556884	0.91[ASN][1000 genomes]
rs4377101	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs4392003	0.86[ASN][1000 genomes]
rs4774220	0.89[ASN][1000 genomes]
rs4774800	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4774802	0.85[CHB][hapmap]
rs492363	0.86[JPT][hapmap]
rs572531	0.83[JPT][hapmap]
rs62043869	0.86[ASN][1000 genomes]
rs6493805	0.86[ASN][1000 genomes]
rs6493807	0.82[ASN][1000 genomes]
rs6493809	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs6493814	0.81[CHB][hapmap]
rs7162879	0.85[CHB][hapmap]
rs7163167	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs7166952	0.81[ASN][1000 genomes]
rs7171318	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7171522	0.80[ASN][1000 genomes]
rs7171834	0.80[ASN][1000 genomes]
rs7172903	0.82[ASN][1000 genomes]
rs7178379	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7181212	0.84[CHB][hapmap]
rs7182733	0.81[CHB][hapmap]
rs7359255	0.81[CHB][hapmap]
rs8025445	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs8034113	0.82[ASN][1000 genomes]
rs8037136	0.85[CHB][hapmap]
rs9920076	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs9920246	0.82[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv457158	chr15:55930542-55982257	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv569541	chr15:55930542-55982257	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11854213	PRTG	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55911800-55977000	Weak transcription	Fetal Intestine Small	intestine
2	chr15:55920800-55987600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:55932600-55987000	Weak transcription	Ovary	ovary
4	chr15:55932800-55973400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:55942800-55974400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:55952800-55972000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:55954000-55971600	Weak transcription	Fetal Kidney	kidney
8	chr15:55954000-55975400	Weak transcription	HSMM	muscle
9	chr15:55954000-55977400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr15:55954400-55987000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:55954600-55975000	Weak transcription	A549	lung
12	chr15:55955400-55980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:55958200-55977600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:55958800-55977400	Weak transcription	Left Ventricle	heart
15	chr15:55959000-55973800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:55960400-55977600	Weak transcription	Placenta	Placenta
17	chr15:55960800-55995800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:55961400-55972400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:55961400-55973000	Weak transcription	Psoas Muscle	Psoas
20	chr15:55962600-55974800	Weak transcription	Fetal Muscle Leg	muscle
21	chr15:55963400-55980200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:55964000-55977200	Weak transcription	HUVEC	blood vessel
23	chr15:55964200-55975600	Weak transcription	Fetal Stomach	stomach
24	chr15:55964800-55977200	Weak transcription	HepG2	liver
25	chr15:55966000-55974400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:55967600-55970600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:55968000-55970800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:55969000-55975600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:55969000-55976000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:55969000-55976800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:55969000-55987000	Weak transcription	Fetal Lung	lung
32	chr15:55969200-55970400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:55969200-55971200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:55969200-55975600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr15:55969200-55980200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:55969200-55986000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:55969400-55980200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:55970000-55970200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr15:55970000-55972000	Strong transcription	Fetal Intestine Large	intestine

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