Variant report

Variant	rs4055
Chromosome Location	chr22:29352495-29352496
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1222	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs13056243	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]
rs13058031	0.94[CEU][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap]
rs13058453	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs132539	0.84[CHD][hapmap];0.82[GIH][hapmap]
rs16986825	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.85[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];0.86[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];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16986864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[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]
rs2267131	0.94[CEU][hapmap]
rs2301428	0.94[CEU][hapmap]
rs28360615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34578331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5752797	0.89[CEU][hapmap]
rs5752803	0.94[CEU][hapmap]
rs5752811	0.94[CEU][hapmap];0.81[TSI][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];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs916332	0.85[AMR][1000 genomes];0.86[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4055	SUSD2	cis	parietal	SCAN
rs4055	MN1	cis	cerebellum	SCAN
rs4055	PIWIL3	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29339800-29352600	Weak transcription	Stomach Mucosa	stomach
2	chr22:29346400-29353800	Weak transcription	NHEK	skin
3	chr22:29346400-29357400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr22:29346600-29352800	Weak transcription	Brain Substantia Nigra	brain
5	chr22:29347600-29356200	Weak transcription	Brain Germinal Matrix	brain
6	chr22:29348200-29353800	Enhancers	Colon Smooth Muscle	Colon
7	chr22:29348200-29365000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr22:29348400-29352600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr22:29348800-29360400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr22:29349200-29356800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr22:29349200-29365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr22:29349200-29371800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr22:29349200-29371800	Weak transcription	HSMM	muscle
14	chr22:29349400-29352600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr22:29349400-29354400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr22:29349400-29354600	Weak transcription	Adipose Nuclei	Adipose
17	chr22:29349400-29357200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr22:29349400-29357400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr22:29349400-29357400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr22:29349600-29352600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr22:29349600-29354400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr22:29349600-29354400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr22:29349600-29354800	Weak transcription	A549	lung
24	chr22:29349600-29357200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr22:29349600-29359600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr22:29349800-29360400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr22:29350000-29352800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr22:29350000-29354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr22:29350000-29354400	Weak transcription	Esophagus	oesophagus
30	chr22:29350000-29354400	Weak transcription	Left Ventricle	heart
31	chr22:29350000-29358400	Weak transcription	Fetal Lung	lung
32	chr22:29350000-29363000	Weak transcription	Liver	Liver
33	chr22:29350000-29372800	Weak transcription	Aorta	Aorta
34	chr22:29350200-29352600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr22:29350200-29354400	Weak transcription	Fetal Kidney	kidney
36	chr22:29350200-29357800	Weak transcription	K562	blood
37	chr22:29350400-29352600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr22:29350400-29354200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr22:29350400-29354600	Weak transcription	Pancreas	Pancrea
40	chr22:29350400-29361000	Weak transcription	Ovary	ovary
41	chr22:29350600-29352800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr22:29350800-29353200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
43	chr22:29350800-29354400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr22:29350800-29357800	Weak transcription	HSMMtube	muscle
45	chr22:29351200-29353000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
46	chr22:29351200-29353000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
47	chr22:29351200-29353000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
48	chr22:29351200-29353200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
49	chr22:29351200-29353200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
50	chr22:29351200-29354200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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