Variant report

Variant	rs17598797
Chromosome Location	chr4:22463486-22463487
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	chr4:22457536..22463707-chr4:22514115..22518559,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152990	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10002842	1.00[JPT][hapmap]
rs10003859	0.83[CEU][hapmap]
rs10003883	0.80[CEU][hapmap]
rs10007714	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10007873	0.81[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10020672	0.82[ASN][1000 genomes]
rs10022239	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025779	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11723133	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12108588	1.00[JPT][hapmap]
rs13108229	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs13129189	0.83[CEU][hapmap]
rs1500451	1.00[JPT][hapmap]
rs1500452	1.00[JPT][hapmap]
rs16872624	1.00[JPT][hapmap]
rs16872654	0.85[MEX][hapmap];0.87[AMR][1000 genomes]
rs17598910	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600487	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs28668190	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4235298	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs6824902	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6833226	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv878752	chr4:22414023-22501043	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17598797	NFKBIL2	trans	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22388400-22473600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:22388800-22469600	Weak transcription	Colonic Mucosa	Colon
3	chr4:22389200-22473600	Weak transcription	Fetal Brain Male	brain
4	chr4:22419200-22476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:22419400-22465800	Weak transcription	HUVEC	blood vessel
6	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
7	chr4:22433800-22479200	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:22437400-22476400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:22437800-22465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:22443400-22471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:22443400-22472400	Weak transcription	Ovary	ovary
12	chr4:22443400-22473600	Weak transcription	Fetal Brain Female	brain
13	chr4:22443600-22470800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:22443600-22476200	Weak transcription	A549	lung
15	chr4:22443800-22474600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:22444000-22470800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:22447200-22467600	Weak transcription	Thymus	Thymus
18	chr4:22447200-22473800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:22447200-22475000	Weak transcription	NHLF	lung
20	chr4:22447800-22473400	Weak transcription	Brain Germinal Matrix	brain
21	chr4:22448600-22472600	Weak transcription	Primary T cells from cord blood	blood
22	chr4:22450200-22471000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:22450200-22473800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:22450200-22473800	Weak transcription	NH-A	brain
25	chr4:22450400-22474800	Weak transcription	Adipose Nuclei	Adipose
26	chr4:22450400-22476000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:22450400-22484000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:22450400-22493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:22450800-22464200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:22451400-22464000	Weak transcription	Fetal Stomach	stomach
31	chr4:22455600-22474200	Weak transcription	Fetal Thymus	thymus
32	chr4:22456400-22476200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:22456600-22466200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:22456800-22466200	Weak transcription	Right Ventricle	heart
35	chr4:22456800-22476000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:22456800-22479000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:22456800-22485000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:22457000-22464200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:22457000-22473600	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:22457200-22473400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:22457200-22473800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:22457600-22473600	Weak transcription	Fetal Lung	lung
43	chr4:22458200-22464600	Weak transcription	Left Ventricle	heart
44	chr4:22458200-22464800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:22458200-22465200	Enhancers	HepG2	liver
46	chr4:22458200-22472200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:22458400-22472000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:22460200-22472400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:22460400-22469400	Weak transcription	HSMM	muscle
50	chr4:22460400-22470800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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