Variant report

Variant	rs13129571
Chromosome Location	chr4:100472004-100472005
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11097666	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13135675	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13135826	0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13142452	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13151234	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17029189	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17029211	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17029213	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17029215	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17029260	0.86[EUR][1000 genomes]
rs17029263	0.86[EUR][1000 genomes]
rs34135026	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34246356	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34678000	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34734558	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34756677	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34777713	0.81[EUR][1000 genomes]
rs34870956	0.86[EUR][1000 genomes]
rs34874297	0.86[EUR][1000 genomes]
rs35074439	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35189300	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35391161	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35402611	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35561084	0.80[EUR][1000 genomes]
rs35595171	0.80[EUR][1000 genomes]
rs35661838	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35824615	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35826214	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35992230	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41275719	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6532821	1.00[GIH][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6825904	0.86[EUR][1000 genomes]
rs6851824	0.86[EUR][1000 genomes]
rs71612697	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71612700	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71612702	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71614603	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71619723	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7665414	1.00[GIH][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7667001	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7688278	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7695727	0.86[EUR][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	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv3584519	chr4:100323870-100477462	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3584523	chr4:100437553-100476549	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv933074	chr4:100460951-100630600	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100458600-100484000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:100459400-100472200	Weak transcription	Liver	Liver
3	chr4:100459400-100477000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:100462200-100472800	Weak transcription	Psoas Muscle	Psoas
5	chr4:100462200-100483800	Weak transcription	Fetal Intestine Large	intestine
6	chr4:100464600-100483800	Weak transcription	Primary T cells from cord blood	blood
7	chr4:100464800-100484000	Weak transcription	HMEC	breast
8	chr4:100465200-100473600	Weak transcription	Adipose Nuclei	Adipose
9	chr4:100465400-100484000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:100465800-100473200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:100466600-100484000	Weak transcription	Aorta	Aorta
12	chr4:100466800-100476400	Weak transcription	Left Ventricle	heart
13	chr4:100466800-100479600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:100466800-100483800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:100467200-100472200	Weak transcription	Primary B cells from cord blood	blood
16	chr4:100467200-100484200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:100468000-100483600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr4:100468200-100476800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:100468400-100472400	Weak transcription	Fetal Lung	lung
20	chr4:100468400-100475800	Weak transcription	HSMM	muscle
21	chr4:100468400-100484000	Weak transcription	Brain Anterior Caudate	brain
22	chr4:100468600-100483800	Weak transcription	Pancreas	Pancrea
23	chr4:100468600-100483800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:100468600-100484000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:100468600-100484200	Weak transcription	Ovary	ovary
26	chr4:100468800-100483800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:100469000-100475400	Weak transcription	Fetal Kidney	kidney
28	chr4:100469000-100484000	Weak transcription	Lung	lung
29	chr4:100469000-100484200	Weak transcription	NHDF-Ad	bronchial
30	chr4:100469200-100482000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr4:100469800-100483800	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:100470600-100472400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:100470600-100473600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:100470600-100480600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:100470800-100473400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr4:100470800-100484000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr4:100470800-100484000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr4:100471000-100483600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:100471000-100484000	Weak transcription	Brain Substantia Nigra	brain
40	chr4:100471400-100483800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr4:100471400-100484000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:100471600-100483800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:100471800-100483800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr4:100472000-100472800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:100472000-100483600	Weak transcription	K562	blood

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