Variant report

Variant	rs904160
Chromosome Location	chr2:47477584-47477585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47477055..47479211-chr2:47498989..47500882,2	MCF-7	breast:
2	chr2:47471172..47473317-chr2:47476209..47479649,3	MCF-7	breast:
3	chr2:47473511..47478428-chr2:47483950..47488018,4	MCF-7	breast:
4	chr2:47475912..47477732-chr2:47481977..47484022,2	K562	blood:
5	chr2:47401347..47405305-chr2:47474858..47480763,8	MCF-7	breast:
6	chr2:47418320..47420689-chr2:47477088..47480602,4	MCF-7	breast:
7	chr2:47400916..47405681-chr2:47469986..47480951,19	K562	blood:
8	chr2:47441944..47444316-chr2:47476312..47479303,2	MCF-7	breast:
9	chr2:47476493..47480049-chr2:47496667..47500826,6	MCF-7	breast:
10	chr2:47400516..47406880-chr2:47471949..47486822,24	K562	blood:
11	chr2:47450507..47453723-chr2:47476153..47479003,3	MCF-7	breast:
12	chr2:47465412..47469681-chr2:47474773..47478680,4	MCF-7	breast:
13	chr2:47409469..47411339-chr2:47477135..47479722,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226087	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10169164	0.87[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1995109	0.94[CHB][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1995110	0.90[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4952879	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953484	0.82[ASN][1000 genomes]
rs4953485	0.82[ASN][1000 genomes]
rs6748764	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7560679	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7598661	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv526478	chr2:47476816-47477584	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47475800-47478600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:47475800-47478800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:47476000-47477600	Enhancers	Hela-S3	cervix
4	chr2:47476000-47478000	Enhancers	Fetal Muscle Leg	muscle
5	chr2:47476000-47478200	Enhancers	HSMM	muscle
6	chr2:47476000-47479400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:47476400-47478000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:47476400-47478000	Enhancers	Duodenum Mucosa	Duodenum
9	chr2:47476400-47478200	Enhancers	NH-A	brain
10	chr2:47476600-47478000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr2:47476600-47478600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:47476600-47483800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:47476800-47477800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:47476800-47478200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:47476800-47483600	Weak transcription	A549	lung
16	chr2:47477000-47483400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:47477000-47483400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:47477000-47491400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:47477200-47491200	Weak transcription	Brain Anterior Caudate	brain
20	chr2:47477400-47477600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr2:47477400-47477800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr2:47477400-47479600	Weak transcription	Fetal Intestine Small	intestine

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