Variant report

Variant	rs5997592
Chromosome Location	chr22:30609096-30609097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30584661..30587555-chr22:30606550..30610248,3	MCF-7	breast:
2	chr22:30604426..30607194-chr22:30608754..30611954,4	K562	blood:

Extended variants
information (count: 8 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs35967341	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614162	1.00[ASW][hapmap];0.84[MKK][hapmap]
rs9614163	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5997592	SEC14L3	cis	parietal	SCAN
rs5997592	MTMR3	cis	parietal	SCAN
rs5997592	LRP5L	cis	cerebellum	SCAN
rs5997592	GATSL3	cis	cerebellum	SCAN
rs5997592	KIAA1671	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30597600-30609800	Enhancers	Stomach Mucosa	stomach
2	chr22:30597600-30610000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr22:30600400-30610000	Enhancers	HMEC	breast
4	chr22:30601000-30610000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr22:30601800-30609800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr22:30601800-30610400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr22:30603000-30609800	Enhancers	Osteobl	bone
8	chr22:30603400-30610600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr22:30603600-30610600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr22:30603800-30613600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:30605000-30609600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr22:30605400-30609400	Weak transcription	Colonic Mucosa	Colon
13	chr22:30605400-30613400	Weak transcription	Aorta	Aorta
14	chr22:30605600-30610600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr22:30605600-30622600	Weak transcription	Right Atrium	heart
16	chr22:30606000-30609200	Weak transcription	Ovary	ovary
17	chr22:30606000-30609800	Enhancers	Esophagus	oesophagus
18	chr22:30606800-30609600	Enhancers	HSMM	muscle
19	chr22:30606800-30613800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr22:30607000-30609200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr22:30607000-30609200	Enhancers	Hela-S3	cervix
22	chr22:30607000-30610000	Enhancers	HepG2	liver
23	chr22:30607000-30610600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr22:30607000-30610600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr22:30607400-30609400	Enhancers	Gastric	stomach
26	chr22:30607600-30609600	Enhancers	Pancreas	Pancrea
27	chr22:30607800-30609600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr22:30607800-30609600	Enhancers	Lung	lung
29	chr22:30607800-30610400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr22:30608000-30609600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr22:30608000-30609800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr22:30608000-30609800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr22:30608200-30609200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr22:30608200-30609200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr22:30608200-30609800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr22:30608200-30609800	Enhancers	NHLF	lung
37	chr22:30608200-30610000	Enhancers	NH-A	brain
38	chr22:30608400-30609200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr22:30608400-30609400	Enhancers	Brain Hippocampus Middle	brain
40	chr22:30608400-30609400	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr22:30608400-30609400	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr22:30608400-30609400	Enhancers	K562	blood
43	chr22:30608400-30609600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr22:30608400-30609600	Enhancers	Primary hematopoietic stem cells	blood
45	chr22:30608400-30609600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr22:30608400-30609600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr22:30608400-30609600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr22:30608400-30609600	Bivalent Enhancer	Adipose Nuclei	Adipose
49	chr22:30608400-30609600	Enhancers	Duodenum Mucosa	Duodenum
50	chr22:30608400-30609600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle

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