Variant report

Variant	rs13056243
Chromosome Location	chr22:29349306-29349307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1222	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs13058031	0.94[CEU][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap]
rs13058453	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132539	0.84[CHD][hapmap]
rs16986825	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16986838	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16986861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16986864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267131	0.94[CEU][hapmap]
rs2301428	0.94[CEU][hapmap]
rs28360615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34578331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752797	0.89[CEU][hapmap]
rs5752803	0.94[CEU][hapmap]
rs5752811	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs5762780	0.87[CEU][hapmap]
rs5762799	0.89[CEU][hapmap]
rs5762814	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs5762816	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs739196	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs916332	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13056243	PIWIL3	cis	parietal	SCAN
rs13056243	FLJ33814	cis	multi-tissue	Pritchard
rs13056243	SUSD2	cis	parietal	SCAN
rs13056243	MN1	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29339800-29352600	Weak transcription	Stomach Mucosa	stomach
2	chr22:29345200-29350800	Enhancers	Fetal Muscle Leg	muscle
3	chr22:29345400-29349800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr22:29345400-29350000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr22:29345400-29350000	Enhancers	Fetal Lung	lung
6	chr22:29345600-29349600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr22:29345600-29350200	Enhancers	Fetal Kidney	kidney
8	chr22:29345800-29349400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr22:29345800-29349800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr22:29345800-29350000	Enhancers	Rectal Smooth Muscle	rectum
11	chr22:29345800-29350600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr22:29345800-29351200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr22:29346000-29350000	Enhancers	Liver	Liver
14	chr22:29346400-29353800	Weak transcription	NHEK	skin
15	chr22:29346400-29357400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr22:29346600-29352800	Weak transcription	Brain Substantia Nigra	brain
17	chr22:29347000-29350800	Enhancers	Placenta	Placenta
18	chr22:29347200-29349600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr22:29347200-29350400	Enhancers	Osteobl	bone
20	chr22:29347400-29349400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr22:29347400-29349400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr22:29347400-29349400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr22:29347400-29349400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr22:29347400-29350000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr22:29347400-29350400	Enhancers	Fetal Intestine Large	intestine
26	chr22:29347400-29350400	Genic enhancers	Fetal Intestine Small	intestine
27	chr22:29347400-29350400	Enhancers	Ovary	ovary
28	chr22:29347600-29349400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr22:29347600-29349400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr22:29347600-29349400	Enhancers	Fetal Muscle Trunk	muscle
31	chr22:29347600-29349600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr22:29347600-29349800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr22:29347600-29350000	Enhancers	Fetal Stomach	stomach
34	chr22:29347600-29350200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr22:29347600-29350200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr22:29347600-29350400	Enhancers	Psoas Muscle	Psoas
37	chr22:29347600-29356200	Weak transcription	Brain Germinal Matrix	brain
38	chr22:29347800-29349400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr22:29347800-29349400	Enhancers	Placenta Amnion	Placenta Amnion
40	chr22:29347800-29349600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr22:29347800-29349600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr22:29347800-29349600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr22:29347800-29350000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr22:29347800-29350400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr22:29348000-29350400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr22:29348000-29350800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr22:29348000-29352400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr22:29348200-29349400	Enhancers	Adipose Nuclei	Adipose
49	chr22:29348200-29349600	Enhancers	A549	lung
50	chr22:29348200-29349600	Enhancers	Hela-S3	cervix

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