Variant report

Variant	rs5994329
Chromosome Location	chr22:31049070-31049071
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11914089	0.93[ASN][1000 genomes]
rs12168004	0.90[ASN][1000 genomes]
rs13433541	0.90[ASN][1000 genomes]
rs16988855	0.84[JPT][hapmap]
rs16988936	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2013928	0.93[ASN][1000 genomes]
rs2072195	0.82[ASN][1000 genomes]
rs2267162	0.83[JPT][hapmap]
rs2283873	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs55844758	0.92[ASN][1000 genomes]
rs5997719	0.93[ASN][1000 genomes]
rs5997722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap]
rs5997728	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72558391	0.82[ASN][1000 genomes]
rs7290898	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs8135379	0.90[ASN][1000 genomes]
rs8135450	0.91[ASN][1000 genomes]
rs9306264	0.90[ASN][1000 genomes]
rs9606761	0.95[ASN][1000 genomes]
rs9606762	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9619128	0.88[ASN][1000 genomes]
rs9621051	0.90[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	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs5994329	HORMAD2	cis	cerebellum	SCAN
rs5994329	LIF	cis	parietal	SCAN
rs5994329	OSBP2	cis	parietal	SCAN
rs5994329	RNF185	cis	parietal	SCAN
rs5994329	SEZ6L	cis	cerebellum	SCAN
rs5994329	TCN2	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31032400-31052400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:31033200-31052000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:31033400-31058200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr22:31033600-31058000	Weak transcription	Adipose Nuclei	Adipose
5	chr22:31033600-31058000	Weak transcription	Fetal Lung	lung
6	chr22:31033800-31057600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr22:31034000-31049800	Weak transcription	Fetal Brain Female	brain
8	chr22:31034000-31059400	Weak transcription	Aorta	Aorta
9	chr22:31034200-31057800	Weak transcription	Colon Smooth Muscle	Colon
10	chr22:31034200-31058800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr22:31039400-31050600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr22:31040200-31060800	Weak transcription	Fetal Brain Male	brain
13	chr22:31040600-31055800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr22:31043600-31055400	Weak transcription	Fetal Stomach	stomach
15	chr22:31043800-31051600	Weak transcription	Primary T cells from cord blood	blood
16	chr22:31044200-31050400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr22:31044200-31057600	Weak transcription	Ovary	ovary
18	chr22:31044200-31058000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr22:31045200-31062800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:31045400-31057600	Weak transcription	Colonic Mucosa	Colon
21	chr22:31045400-31057600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr22:31045400-31062800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr22:31045400-31062800	Weak transcription	NH-A	brain
24	chr22:31045600-31058200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr22:31045600-31062800	Weak transcription	HSMMtube	muscle
26	chr22:31045800-31050200	Weak transcription	Spleen	Spleen
27	chr22:31045800-31050400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr22:31045800-31057600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr22:31045800-31057800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr22:31045800-31061400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr22:31045800-31062200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr22:31046000-31050200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr22:31046000-31054800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr22:31046000-31057600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr22:31046000-31057600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr22:31046000-31057600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr22:31046000-31057600	Weak transcription	NHDF-Ad	bronchial
38	chr22:31046000-31057800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr22:31046000-31057800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr22:31046000-31057800	Weak transcription	Osteobl	bone
41	chr22:31046000-31058000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr22:31046000-31058400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr22:31046000-31062000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr22:31046000-31062200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr22:31046000-31062600	Weak transcription	HMEC	breast
46	chr22:31046000-31062600	Weak transcription	NHLF	lung
47	chr22:31046800-31050200	Weak transcription	Brain Germinal Matrix	brain
48	chr22:31046800-31057600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr22:31046800-31057600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr22:31046800-31057600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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