Variant report

Variant	rs11896275
Chromosome Location	chr2:47485134-47485135
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47478646..47481044-chr2:47483765..47486319,2	MCF-7	breast:
2	chr2:47399035..47407354-chr2:47479551..47494841,29	MCF-7	breast:
3	chr2:47400516..47406880-chr2:47471949..47486822,24	K562	blood:
4	chr2:47484967..47487278-chr2:47489027..47491218,2	MCF-7	breast:
5	chr2:47401545..47404971-chr2:47483615..47487701,5	MCF-7	breast:
6	chr2:47484144..47487627-chr2:47488980..47491395,3	K562	blood:
7	chr2:47484907..47487691-chr2:47537998..47540453,2	MCF-7	breast:
8	chr2:47399224..47401292-chr2:47482890..47486794,3	MCF-7	breast:
9	chr2:47401084..47403383-chr2:47484393..47487548,4	K562	blood:
10	chr2:47473511..47478428-chr2:47483950..47488018,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10168806	0.83[EUR][1000 genomes]
rs10172988	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174718	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10185578	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10186190	0.86[CHB][hapmap]
rs10190105	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10209219	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10209762	0.87[CHB][hapmap]
rs11125127	0.91[ASN][1000 genomes]
rs11125128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885910	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11894768	0.80[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs11900317	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12612772	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12618281	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553061	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17036412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036164	0.83[ASN][1000 genomes]
rs6727256	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6738753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755555	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806423	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7595170	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7595256	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	esv3445763	chr2:47485075-47485305	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47477000-47491400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:47477200-47491200	Weak transcription	Brain Anterior Caudate	brain
3	chr2:47478800-47487400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:47478800-47496400	Weak transcription	Hela-S3	cervix
5	chr2:47480000-47486600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:47482400-47489400	Weak transcription	Fetal Intestine Small	intestine
7	chr2:47482400-47491400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:47483400-47485200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:47483400-47485600	Enhancers	HSMM	muscle
10	chr2:47483400-47485800	Enhancers	HSMMtube	muscle
11	chr2:47483800-47485200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:47483800-47492000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:47484000-47487200	Weak transcription	Spleen	Spleen
14	chr2:47484000-47487800	Weak transcription	Placenta	Placenta
15	chr2:47484200-47485400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:47484200-47491200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:47484200-47491600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:47484600-47485400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:47485000-47485200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr2:47485000-47485200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:47485000-47485200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:47485000-47485600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:47485000-47485600	Enhancers	GM12878-XiMat	blood

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