Variant report

Variant	rs10939936
Chromosome Location	chr5:61638835-61638836
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61561863..61563479-chr5:61638036..61640734,2	K562	blood:
2	chr5:61637038..61639616-chr5:61644276..61647073,2	MCF-7	breast:
3	chr5:61638389..61640483-chr5:61640496..61643629,3	K562	blood:
4	chr5:61602330..61604581-chr5:61636103..61640000,3	K562	blood:
5	chr5:61602330..61604453-chr5:61636103..61638930,2	K562	blood:
6	chr5:61629672..61632580-chr5:61634669..61639677,5	K562	blood:

Variant related genes	Relation type
ENSG00000068796	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10062264	0.94[AFR][1000 genomes]
rs10079409	0.91[ASN][1000 genomes]
rs1025032	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10471542	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1054897	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10939938	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12153750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187566	0.99[AFR][1000 genomes]
rs12519766	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12658256	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12696991	0.96[AFR][1000 genomes]
rs153868	0.92[AFR][1000 genomes]
rs16890656	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808400	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1848504	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2063256	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2257389	0.89[AFR][1000 genomes]
rs2272290	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2463078	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs264522	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264524	0.96[AFR][1000 genomes]
rs264525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs264526	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264529	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs264532	0.96[AFR][1000 genomes]
rs28720674	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs37032	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3842912	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3846468	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3857259	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3892140	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700491	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6863617	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6864450	0.90[ASN][1000 genomes]
rs6872078	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6884054	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73104056	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73104058	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7729719	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7734679	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9291759	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9981	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' 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
3	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv881726	chr5:61556730-61676911	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv881727	chr5:61578041-61700970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61603400-61658600	Weak transcription	Aorta	Aorta
2	chr5:61604400-61643800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:61604600-61658600	Weak transcription	Fetal Kidney	kidney
4	chr5:61607800-61669400	Weak transcription	NHLF	lung
5	chr5:61610200-61658600	Weak transcription	Ovary	ovary
6	chr5:61611600-61639000	Weak transcription	HMEC	breast
7	chr5:61611600-61643800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:61612000-61642400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:61612000-61661000	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:61615600-61658600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:61618200-61647800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr5:61618400-61658600	Weak transcription	Hela-S3	cervix
13	chr5:61622400-61676000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:61622600-61643800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:61622600-61658800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:61623000-61643000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:61623000-61646200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:61623800-61643800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:61623800-61658600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:61624000-61669600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:61625400-61644000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:61625400-61646200	Weak transcription	Adipose Nuclei	Adipose
23	chr5:61626600-61639000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:61628200-61644400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:61628800-61652000	Weak transcription	Fetal Brain Female	brain
26	chr5:61629200-61676400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:61629600-61645600	Weak transcription	HSMMtube	muscle
28	chr5:61629600-61665000	Weak transcription	Esophagus	oesophagus
29	chr5:61629800-61643200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr5:61629800-61659400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:61630200-61646000	Weak transcription	Fetal Brain Male	brain
32	chr5:61630600-61643800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:61630600-61644000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:61630800-61643600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:61631000-61644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:61631000-61658400	Weak transcription	Colonic Mucosa	Colon
37	chr5:61631200-61642600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:61631200-61643600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:61631200-61643800	Weak transcription	HSMM	muscle
40	chr5:61631200-61644000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:61631200-61644200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:61631200-61645800	Weak transcription	Brain Anterior Caudate	brain
43	chr5:61631200-61646000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr5:61631200-61646200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr5:61631200-61646200	Weak transcription	Spleen	Spleen
46	chr5:61631200-61658800	Weak transcription	Pancreas	Pancrea
47	chr5:61631200-61669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:61631200-61669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:61631200-61676000	Weak transcription	Lung	lung
50	chr5:61631400-61639200	Weak transcription	Muscle Satellite Cultured Cells	--

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