Variant report

Variant	rs40060
Chromosome Location	chr5:74967386-74967387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74633002..74635499-chr5:74966644..74968332,2	K562	blood:
2	chr5:74786766..74788653-chr5:74965428..74967574,2	K562	blood:

Variant related genes	Relation type
ENSG00000113161	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10057967	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10075465	0.94[ASW][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10515214	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs16872768	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2112347	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs253391	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs253411	0.96[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs253412	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs253414	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34351	0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34359	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34360	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34361	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3797580	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3815895	0.81[AFR][1000 genomes]
rs42302	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs42854	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4549504	0.81[GIH][hapmap]
rs4604177	0.81[GIH][hapmap]
rs4704230	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6864091	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6874626	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6881648	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6893029	0.81[AFR][1000 genomes]
rs888786	0.88[ASW][hapmap];1.00[YRI][hapmap];0.80[AFR][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	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv522003	chr5:74947435-74988369	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830353	chr5:74961520-75152609	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74952800-74981400	Weak transcription	Psoas Muscle	Psoas
2	chr5:74960200-74968600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:74961000-74976800	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:74961000-74987800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:74961200-74968000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:74962000-74979400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:74963000-74989800	Weak transcription	Esophagus	oesophagus
8	chr5:74963200-74976600	Weak transcription	HMEC	breast
9	chr5:74963400-74968600	Weak transcription	Fetal Lung	lung
10	chr5:74963400-74968600	Weak transcription	Ovary	ovary
11	chr5:74963800-74968200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:74964000-74968200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:74964400-74967400	Enhancers	Fetal Kidney	kidney
14	chr5:74964600-74970800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:74964800-74989400	Weak transcription	HSMMtube	muscle
16	chr5:74965000-74968400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:74965000-74968400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:74965000-74968800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:74965000-74976600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:74965000-74977000	Weak transcription	Brain Angular Gyrus	brain
21	chr5:74965000-74978600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:74965000-74979800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:74965000-74983800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:74965000-74991200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr5:74965000-74998000	Weak transcription	Fetal Brain Female	brain
26	chr5:74965200-74968200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:74965200-74968200	Weak transcription	Brain Substantia Nigra	brain
28	chr5:74965200-74968400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr5:74965200-74968400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:74965200-74977000	Weak transcription	NHLF	lung
31	chr5:74965200-75011800	Weak transcription	Brain Germinal Matrix	brain
32	chr5:74965400-74967800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr5:74965400-74968000	Weak transcription	Placenta	Placenta
34	chr5:74965400-74968200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr5:74965400-74968200	Weak transcription	Fetal Muscle Leg	muscle
36	chr5:74965400-74968200	Weak transcription	Left Ventricle	heart
37	chr5:74965400-74968400	Weak transcription	Adipose Nuclei	Adipose
38	chr5:74965400-74968400	Weak transcription	Fetal Stomach	stomach
39	chr5:74965400-74968400	Weak transcription	Fetal Thymus	thymus
40	chr5:74965400-74968600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr5:74965400-74969000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:74965400-74969200	Weak transcription	Aorta	Aorta
43	chr5:74965400-74969800	Weak transcription	Primary B cells from cord blood	blood
44	chr5:74965400-74969800	Weak transcription	Thymus	Thymus
45	chr5:74965400-74970200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:74965400-74970200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:74965400-74970600	Weak transcription	Brain Hippocampus Middle	brain
48	chr5:74965400-74977000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr5:74965400-74977000	Weak transcription	NH-A	brain
50	chr5:74965400-74978000	Weak transcription	Rectal Smooth Muscle	rectum

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