Variant report

Variant	rs6874260
Chromosome Location	chr5:126747583-126747584
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10491250	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10519935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11745840	1.00[CEU][hapmap]
rs12109001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1363384	1.00[ASN][1000 genomes]
rs1363386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1501993	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1529468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17164854	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17164923	1.00[CEU][hapmap]
rs17164951	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17165013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17165018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17165019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17684644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17684655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17684679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17684691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17684740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17684775	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17763126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17763172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1990954	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1990955	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2042941	1.00[ASN][1000 genomes]
rs2042942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2042943	1.00[ASN][1000 genomes]
rs2270933	1.00[CEU][hapmap]
rs3851468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41298316	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56157640	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60681812	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60998265	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6865700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6897163	1.00[CEU][hapmap]
rs73346906	0.80[ASN][1000 genomes]
rs73348744	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7715710	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7737871	1.00[CEU][hapmap]
rs929781	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs929782	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126734800-126753400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:126742800-126754000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:126742800-126760200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:126742800-126762600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:126742800-126782000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:126742800-126792400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:126743000-126755600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:126743000-126784800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:126743400-126760000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:126745600-126748400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:126746000-126748400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:126746000-126749400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:126746200-126748000	Strong transcription	Brain Anterior Caudate	brain
14	chr5:126746200-126748800	Strong transcription	HSMMtube	muscle
15	chr5:126746200-126752200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:126746200-126754800	Weak transcription	Psoas Muscle	Psoas
17	chr5:126746200-126758000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:126746400-126752200	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:126746400-126752200	Weak transcription	Brain Substantia Nigra	brain
20	chr5:126746400-126752400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:126746400-126752400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:126746400-126752800	Weak transcription	Brain Angular Gyrus	brain
23	chr5:126746400-126760800	Weak transcription	HSMM	muscle
24	chr5:126746600-126749200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:126746600-126752600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr5:126747000-126748400	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:126747000-126755000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:126747000-126759200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:126747200-126755000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr5:126747400-126747600	Weak transcription	Fetal Lung	lung
31	chr5:126747400-126752800	Weak transcription	Fetal Brain Male	brain

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