Variant report

Variant	rs1401780
Chromosome Location	chr2:152741725-152741726
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	chr2:152734671..152737865-chr2:152741650..152744701,3	K562	blood:
2	chr2:152684319..152686783-chr2:152740216..152743697,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162980	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10178110	0.86[CEU][hapmap]
rs10184416	0.83[CEU][hapmap]
rs11695363	1.00[YRI][hapmap]
rs12471646	0.87[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs13394161	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13421962	0.83[CEU][hapmap]
rs17270290	0.83[CEU][hapmap]
rs2461835	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680976	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35343813	0.82[JPT][hapmap]
rs36052741	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4524119	0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4664067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4664508	0.91[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs6729612	0.86[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6729655	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6734642	0.82[JPT][hapmap]
rs6748807	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6756645	0.83[CEU][hapmap]
rs7349251	0.82[JPT][hapmap]
rs7571637	0.82[JPT][hapmap]
rs7598593	0.82[JPT][hapmap]
rs908937	0.83[CEU][hapmap]
rs952340	0.82[JPT][hapmap]
rs956745	0.91[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][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	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 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	chr2:152699800-152742000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:152713000-152747800	Weak transcription	Brain Germinal Matrix	brain
3	chr2:152723000-152748200	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:152730800-152748000	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:152731200-152743400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:152732000-152742600	Weak transcription	Esophagus	oesophagus
7	chr2:152735400-152748200	Weak transcription	Brain Substantia Nigra	brain
8	chr2:152736200-152742200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr2:152736200-152742400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr2:152736400-152742600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:152737000-152742000	Weak transcription	HUVEC	blood vessel
12	chr2:152737400-152748000	Weak transcription	Brain Anterior Caudate	brain
13	chr2:152737600-152747800	Weak transcription	Brain Angular Gyrus	brain
14	chr2:152739200-152742600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:152739600-152748400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:152739600-152753000	Weak transcription	Lung	lung
17	chr2:152739800-152742800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:152739800-152747800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:152739800-152747800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:152739800-152748200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:152740000-152742600	Weak transcription	HepG2	liver
22	chr2:152740000-152742800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:152740000-152748200	Weak transcription	Fetal Brain Female	brain

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