Variant report

Variant	rs334601
Chromosome Location	chr2:179175022-179175023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179173533..179176189-chr2:179203124..179204726,2	K562	blood:
2	chr2:179174181..179176403-chr2:179187172..179189401,2	MCF-7	breast:
3	chr2:179174805..179177159-chr2:179180996..179182677,2	MCF-7	breast:
4	chr2:179173279..179175264-chr2:179179066..179181987,2	K562	blood:

Variant related genes	Relation type
ENSG00000079156	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12471986	1.00[CHB][hapmap]
rs13401080	0.85[EUR][1000 genomes]
rs1368903	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1368907	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1434081	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16866260	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16866263	1.00[JPT][hapmap]
rs16866274	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16866276	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs334595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334605	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334607	1.00[CHB][hapmap]
rs334609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334610	0.86[EUR][1000 genomes]
rs334615	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334619	1.00[JPT][hapmap]
rs4893851	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4894007	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4894010	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6433718	1.00[CHB][hapmap]
rs6433719	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6725937	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6756568	1.00[EUR][1000 genomes]
rs7585689	1.00[CHB][hapmap];1.00[CHD][hapmap];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	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179143200-179188600	Weak transcription	Brain Anterior Caudate	brain
2	chr2:179160200-179188600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:179162400-179179800	Weak transcription	Liver	Liver
4	chr2:179164200-179180400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:179164600-179200800	Weak transcription	Aorta	Aorta
6	chr2:179165200-179177800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:179166800-179179400	Weak transcription	Psoas Muscle	Psoas
8	chr2:179167000-179179400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:179167000-179179400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:179171000-179179000	Weak transcription	Brain Angular Gyrus	brain
11	chr2:179171600-179175800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:179171600-179182000	Weak transcription	HSMM	muscle
13	chr2:179171800-179179800	Weak transcription	K562	blood
14	chr2:179173400-179179400	Weak transcription	Left Ventricle	heart
15	chr2:179174200-179176200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:179174600-179175600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:179174600-179177600	Weak transcription	HMEC	breast

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