Variant report

Variant	rs1653801
Chromosome Location	chr2:134353706-134353707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MGAT5-5	chr2:134353662-134353970	NONHSAT074550

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10194577	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691839	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987374	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13021524	1.00[CHB][hapmap]
rs1432282	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1653797	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1653799	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1653800	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1653802	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1653803	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1653804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669454	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1669458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669460	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4954069	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6430434	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760534	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72849430	1.00[ASN][1000 genomes]
rs7607909	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891822	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv516644	chr2:134301130-134391214	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv431713	chr2:134316522-134413604	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134345400-134360000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:134345400-134360000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:134345800-134357200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:134349000-134354600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:134349200-134354000	Weak transcription	Brain Anterior Caudate	brain
6	chr2:134349200-134354200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:134349200-134354200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:134349200-134354200	Weak transcription	Fetal Brain Female	brain
9	chr2:134349200-134354400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:134349200-134356400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:134349400-134353800	Weak transcription	Brain Substantia Nigra	brain
12	chr2:134349400-134354600	Weak transcription	Brain Angular Gyrus	brain
13	chr2:134349400-134356400	Weak transcription	Brain Germinal Matrix	brain
14	chr2:134349400-134356800	Weak transcription	Fetal Brain Male	brain
15	chr2:134349400-134357200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:134349800-134354600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:134350000-134354200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:134350200-134354400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:134350200-134356000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:134350200-134356000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:134350400-134355800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:134352200-134360000	Weak transcription	NHEK	skin
23	chr2:134352800-134354200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:134353400-134354200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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