Variant report

Variant	rs17558224
Chromosome Location	chr2:47483729-47483730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47482267..47483917-chr2:47489154..47492083,2	MCF-7	breast:
2	chr2:47399035..47407354-chr2:47479551..47494841,29	MCF-7	breast:
3	chr2:47475912..47477732-chr2:47481977..47484022,2	K562	blood:
4	chr2:47400516..47406880-chr2:47471949..47486822,24	K562	blood:
5	chr2:47419209..47420716-chr2:47482219..47483984,2	MCF-7	breast:
6	chr2:47401545..47404971-chr2:47483615..47487701,5	MCF-7	breast:
7	chr2:47399224..47401292-chr2:47482890..47486794,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10165172	1.00[JPT][hapmap]
rs10165417	1.00[JPT][hapmap]
rs10169583	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10175425	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10204202	1.00[JPT][hapmap]
rs10210030	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12328197	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12329350	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13383452	1.00[CHB][hapmap]
rs13383554	1.00[JPT][hapmap]
rs13383815	0.93[ASN][1000 genomes]
rs13386635	1.00[JPT][hapmap]
rs13412502	1.00[JPT][hapmap]
rs13413278	1.00[JPT][hapmap]
rs13424194	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13424419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55741238	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56218686	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56239993	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56406340	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6749044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6751819	1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs931638	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs931640	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3393036	chr2:47482098-47484471	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3354893	chr2:47482498-47483996	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47476600-47483800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr2:47477000-47491400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:47477200-47491200	Weak transcription	Brain Anterior Caudate	brain
4	chr2:47478600-47483800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:47478800-47487400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:47478800-47496400	Weak transcription	Hela-S3	cervix
7	chr2:47480000-47486600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:47481400-47484000	Weak transcription	Fetal Intestine Large	intestine
9	chr2:47482200-47485000	Weak transcription	GM12878-XiMat	blood
10	chr2:47482400-47489400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:47482400-47491400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:47483400-47484200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:47483400-47484200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr2:47483400-47484200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:47483400-47484400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:47483400-47484600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr2:47483400-47484600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:47483400-47484600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:47483400-47485200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:47483400-47485600	Enhancers	HSMM	muscle
21	chr2:47483400-47485800	Enhancers	HSMMtube	muscle
22	chr2:47483600-47483800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:47483600-47483800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr2:47483600-47484000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr2:47483600-47484000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:47483600-47484000	Enhancers	Placenta	Placenta
27	chr2:47483600-47484000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr2:47483600-47484200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr2:47483600-47484200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:47483600-47484200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr2:47483600-47484200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:47483600-47484200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:47483600-47484200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:47483600-47484200	Enhancers	Brain Angular Gyrus	brain
35	chr2:47483600-47484200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:47483600-47484200	Enhancers	NH-A	brain
37	chr2:47483600-47484400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr2:47483600-47484400	Enhancers	Brain Cingulate Gyrus	brain
39	chr2:47483600-47484400	Enhancers	A549	lung
40	chr2:47483600-47484400	Bivalent Enhancer	HepG2	liver

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