Variant report

Variant	rs62406981
Chromosome Location	chr5:179639886-179639887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr5:179639511-179640461	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179638635..179640906-chr5:179719445..179721732,2	K562	blood:

Variant related genes	Relation type
RASGEF1C	TF binding region
ENSG00000248367	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17627815	0.86[ASN][1000 genomes]
rs17627880	0.86[ASN][1000 genomes]
rs34763496	0.84[EUR][1000 genomes]
rs35067749	0.86[ASN][1000 genomes]
rs35211991	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36062422	0.86[EUR][1000 genomes]
rs4700726	0.80[EUR][1000 genomes]
rs55934730	0.83[AFR][1000 genomes]
rs55944951	1.00[AFR][1000 genomes]
rs62406975	0.82[EUR][1000 genomes]
rs62406979	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406982	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406984	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6869231	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823732	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
2	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
4	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
5	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	esv3339444	chr5:179638546-179643144	Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3353801	chr5:179639246-179642644	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv3381775	chr5:179639346-179642344	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3325478	chr5:179639646-179642344	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179635800-179640000	Weak transcription	Brain Angular Gyrus	brain
2	chr5:179635800-179640600	Weak transcription	Fetal Kidney	kidney
3	chr5:179636600-179640000	Weak transcription	Fetal Brain Male	brain
4	chr5:179636600-179640400	Weak transcription	Fetal Heart	heart
5	chr5:179636800-179640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:179638200-179640600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:179638800-179640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:179639200-179640000	Enhancers	Fetal Intestine Small	intestine
9	chr5:179639200-179640400	Bivalent Enhancer	Fetal Stomach	stomach
10	chr5:179639400-179640000	Enhancers	Right Ventricle	heart
11	chr5:179639400-179640200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:179639400-179640600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:179639400-179640600	Enhancers	Colon Smooth Muscle	Colon
14	chr5:179639400-179640600	Enhancers	Rectal Smooth Muscle	rectum
15	chr5:179639600-179640000	Bivalent Enhancer	Placenta	Placenta
16	chr5:179639600-179640200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr5:179639600-179640200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr5:179639600-179640400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:179639600-179640400	Enhancers	Brain Hippocampus Middle	brain
20	chr5:179639600-179640600	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr5:179639800-179640000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:179639800-179640200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:179639800-179640200	Enhancers	Brain Cingulate Gyrus	brain
24	chr5:179639800-179640400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:179639800-179640400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr5:179639800-179640400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:179639800-179640600	Enhancers	Pancreas	Pancrea
28	chr5:179639800-179641000	Enhancers	Esophagus	oesophagus

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