Variant report

Variant	rs59624407
Chromosome Location	chr3:67428871-67428872
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1120653	0.87[ASN][1000 genomes]
rs11705924	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11706477	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11710648	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11715724	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719613	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13091433	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17046321	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17806805	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2017621	0.86[ASN][1000 genomes]
rs3206427	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3206428	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59619050	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9812440	0.86[ASN][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	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67412400-67453000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:67413200-67441800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:67414200-67438800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:67414400-67470800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:67417200-67432600	Weak transcription	A549	lung
6	chr3:67417400-67435800	Weak transcription	Primary B cells from cord blood	blood
7	chr3:67418400-67432600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:67418600-67434600	Weak transcription	Osteobl	bone
9	chr3:67418600-67442600	Weak transcription	Dnd41	blood
10	chr3:67420000-67432600	Weak transcription	Psoas Muscle	Psoas
11	chr3:67420200-67429400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:67420200-67430400	Weak transcription	Pancreas	Pancrea
13	chr3:67420200-67432200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:67420200-67432600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:67420200-67432800	Weak transcription	Right Ventricle	heart
16	chr3:67420200-67437000	Weak transcription	Spleen	Spleen
17	chr3:67420200-67441600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:67420200-67441800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:67420200-67449600	Weak transcription	HSMM	muscle
20	chr3:67420200-67452000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:67420200-67479400	Weak transcription	Esophagus	oesophagus
22	chr3:67421000-67434600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:67421000-67434800	Weak transcription	Adipose Nuclei	Adipose
24	chr3:67421200-67433200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:67421800-67441800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:67422600-67437200	Weak transcription	HMEC	breast
27	chr3:67422800-67439600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:67423200-67441800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:67424000-67429200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr3:67424000-67432600	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:67424400-67435600	Weak transcription	GM12878-XiMat	blood
32	chr3:67424600-67432800	Weak transcription	Fetal Stomach	stomach
33	chr3:67424600-67433200	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:67424600-67457000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:67424600-67466000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:67424600-67471000	Weak transcription	Colonic Mucosa	Colon
37	chr3:67424800-67430000	Weak transcription	Fetal Intestine Small	intestine
38	chr3:67425000-67465200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:67425000-67474200	Weak transcription	Gastric	stomach
40	chr3:67425600-67443200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:67425800-67456000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:67426000-67430400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:67426000-67431400	Strong transcription	Primary T cells from cord blood	blood
44	chr3:67426200-67429200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:67426600-67434400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:67426800-67432600	Weak transcription	Aorta	Aorta
47	chr3:67426800-67432600	Weak transcription	Fetal Lung	lung
48	chr3:67426800-67438600	Weak transcription	Liver	Liver
49	chr3:67426800-67441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:67427000-67429400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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