Variant report

Variant	rs11575388
Chromosome Location	chr7:50567223-50567224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10228056	1.00[CEU][hapmap]
rs1037351	0.82[JPT][hapmap]
rs11575372	0.93[ASN][1000 genomes]
rs11575383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11575387	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11575422	0.90[ASN][1000 genomes]
rs11575431	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575434	0.97[ASN][1000 genomes]
rs11575441	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763051	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11771860	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17133842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs17133853	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs17133881	1.00[CEU][hapmap]
rs17152014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167363	1.00[CHB][hapmap]
rs2167364	0.82[JPT][hapmap]
rs2329364	1.00[CEU][hapmap]
rs3779084	0.90[JPT][hapmap]
rs4245549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs4947631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs58024888	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58085392	0.97[ASN][1000 genomes]
rs6951648	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs72645710	1.00[ASN][1000 genomes]
rs7791875	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs880028	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription 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
2	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv516640	chr7:50565963-50568735	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11575388	IKZF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50543600-50595000	Weak transcription	Liver	Liver
2	chr7:50560800-50581000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:50565200-50568600	Weak transcription	Gastric	stomach
4	chr7:50565200-50569800	Weak transcription	Right Atrium	heart
5	chr7:50565200-50570000	Weak transcription	Left Ventricle	heart
6	chr7:50565200-50570200	Weak transcription	Lung	lung
7	chr7:50565200-50572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr7:50565400-50568600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr7:50565400-50569800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:50565400-50570000	Weak transcription	Pancreas	Pancrea
12	chr7:50565400-50570000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:50565400-50570000	Enhancers	Hela-S3	cervix
14	chr7:50565600-50569800	Weak transcription	Fetal Lung	lung
15	chr7:50565800-50569000	Strong transcription	HepG2	liver
16	chr7:50565800-50570000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:50566000-50569400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:50566200-50567600	Weak transcription	Fetal Stomach	stomach
19	chr7:50566200-50568400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:50566200-50568400	Weak transcription	Spleen	Spleen
21	chr7:50566200-50568600	Weak transcription	Psoas Muscle	Psoas
22	chr7:50566200-50569400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr7:50566200-50569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:50566200-50569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:50566200-50569600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:50566200-50569800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:50566200-50569800	Weak transcription	Ovary	ovary
28	chr7:50566200-50576000	Weak transcription	Colonic Mucosa	Colon
29	chr7:50566200-50581200	Strong transcription	Fetal Intestine Small	intestine
30	chr7:50566400-50568800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:50566400-50572600	Strong transcription	Fetal Intestine Large	intestine
32	chr7:50566600-50569800	Weak transcription	HUVEC	blood vessel
33	chr7:50566800-50571400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr7:50567200-50568200	Weak transcription	Fetal Muscle Leg	muscle
35	chr7:50567200-50568800	Weak transcription	HMEC	breast

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