Variant report

Variant	rs6889554
Chromosome Location	chr5:126755539-126755540
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126751710..126754052-chr5:126754566..126757264,2	K562	blood:
2	chr5:126753682..126756531-chr5:126759834..126762249,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs2108889	1.00[AMR][1000 genomes]
rs55857193	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56408687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57304460	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58622488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59168209	1.00[AMR][1000 genomes]
rs60007347	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60963225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61170684	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6595772	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6868588	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6885300	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73783767	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73783787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73783789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73783791	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73783792	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73783793	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73783796	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73783799	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73783801	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73783802	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73786110	1.00[AMR][1000 genomes]
rs7702677	1.00[AMR][1000 genomes]
rs7703677	0.86[AFR][1000 genomes];1.00[AMR][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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126742800-126760200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:126742800-126762600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:126742800-126782000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:126742800-126792400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:126743000-126755600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:126743000-126784800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:126743400-126760000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:126746200-126758000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:126746400-126760800	Weak transcription	HSMM	muscle
10	chr5:126747000-126759200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:126748400-126758600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:126752200-126756200	Enhancers	Brain Hippocampus Middle	brain
13	chr5:126752200-126756200	Enhancers	Brain Substantia Nigra	brain
14	chr5:126752800-126755800	Enhancers	Brain Angular Gyrus	brain
15	chr5:126753200-126757400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:126753400-126755600	Enhancers	Fetal Brain Female	brain
17	chr5:126753400-126761000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:126754400-126755800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:126754800-126755800	Enhancers	Psoas Muscle	Psoas
20	chr5:126754800-126756000	Enhancers	Fetal Brain Male	brain
21	chr5:126754800-126756800	Genic enhancers	Fetal Muscle Leg	muscle
22	chr5:126755000-126756000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:126755000-126756000	Genic enhancers	Brain Anterior Caudate	brain
24	chr5:126755000-126756000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:126755000-126756600	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr5:126755000-126761800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:126755200-126756000	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr5:126755200-126756400	Genic enhancers	Brain Cingulate Gyrus	brain
29	chr5:126755200-126757200	Strong transcription	HSMMtube	muscle
30	chr5:126755400-126755800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:126755400-126756000	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr5:126755400-126756400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr5:126755400-126774400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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