Variant report

Variant	rs2617403
Chromosome Location	chr5:68429040-68429041
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1086000	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1086001	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs163190	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs164385	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164565	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164567	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164568	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164706	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2069433	0.93[JPT][hapmap]
rs2637143	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337254	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338682	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338683	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338685	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338686	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350097	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351426	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs367245	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs454528	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56152197	0.92[ASN][1000 genomes]
rs645089	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73119301	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv881765	chr5:68379836-68448694	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv881766	chr5:68401941-68448694	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68391400-68431200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:68400200-68431200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:68402600-68429600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:68406000-68430000	Strong transcription	Liver	Liver
5	chr5:68406200-68438400	Weak transcription	Aorta	Aorta
6	chr5:68406400-68431600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:68410400-68431800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:68412400-68434600	Weak transcription	Psoas Muscle	Psoas
9	chr5:68415600-68431400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:68416400-68445000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:68418400-68429800	Weak transcription	Pancreas	Pancrea
12	chr5:68418600-68431200	Weak transcription	Gastric	stomach
13	chr5:68419200-68429200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:68419200-68431600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:68419400-68430600	Weak transcription	HUVEC	blood vessel
16	chr5:68420600-68434800	Weak transcription	Fetal Brain Male	brain
17	chr5:68421000-68431200	Weak transcription	Brain Angular Gyrus	brain
18	chr5:68421200-68431600	Weak transcription	Spleen	Spleen
19	chr5:68421400-68433400	Weak transcription	Left Ventricle	heart
20	chr5:68421600-68447000	Weak transcription	Ovary	ovary
21	chr5:68421800-68431400	Weak transcription	Lung	lung
22	chr5:68422400-68430000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:68423600-68432600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:68423800-68432200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:68424000-68429600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:68424000-68430200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:68424000-68431000	Weak transcription	HMEC	breast
28	chr5:68424000-68431600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:68424000-68432200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:68424000-68434000	Weak transcription	Brain Germinal Matrix	brain
31	chr5:68424400-68429200	Weak transcription	HSMMtube	muscle
32	chr5:68424400-68433200	Weak transcription	Right Ventricle	heart
33	chr5:68424600-68431400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr5:68424800-68431400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:68425000-68430000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:68425000-68431600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:68425000-68433200	Weak transcription	Thymus	Thymus
38	chr5:68425200-68429400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr5:68425400-68431400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:68425400-68434400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr5:68425600-68431200	Weak transcription	Fetal Lung	lung
42	chr5:68425600-68431200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr5:68425600-68431400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:68425600-68431600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr5:68425600-68432000	Weak transcription	Brain Substantia Nigra	brain
46	chr5:68425600-68432000	Weak transcription	K562	blood
47	chr5:68425600-68432000	Weak transcription	NHEK	skin
48	chr5:68425600-68432200	Weak transcription	Fetal Thymus	thymus
49	chr5:68425600-68433200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr5:68425800-68430800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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