Variant report

Variant	rs13100446
Chromosome Location	chr3:105560072-105560073
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10804442	0.94[AMR][1000 genomes]
rs10933833	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11711088	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12636287	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13060223	0.93[AMR][1000 genomes]
rs13085563	0.92[AMR][1000 genomes]
rs1443102	0.94[AMR][1000 genomes]
rs1470283	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1867195	0.91[AMR][1000 genomes]
rs1992522	0.92[AMR][1000 genomes]
rs2055557	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2099892	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2399056	0.94[AMR][1000 genomes]
rs28427229	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28533328	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3996189	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4243427	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4447799	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4894950	0.93[AMR][1000 genomes]
rs4894953	0.94[AMR][1000 genomes]
rs4894954	0.89[AMR][1000 genomes]
rs4894957	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4894960	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4894962	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6437624	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6788366	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6795961	0.94[AMR][1000 genomes]
rs6807382	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs71627856	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7432372	0.94[AMR][1000 genomes]
rs7637327	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7645021	0.91[AMR][1000 genomes]
rs7647955	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7651784	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs769315	0.94[AMR][1000 genomes]
rs971110	0.91[AMR][1000 genomes]
rs9841500	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[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	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv508234	chr3:105549864-105565806	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
2	chr3:105532200-105563000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:105533600-105560600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:105533800-105570000	Weak transcription	Dnd41	blood
5	chr3:105534200-105566200	Weak transcription	Brain Germinal Matrix	brain
6	chr3:105540800-105569600	Weak transcription	Fetal Thymus	thymus
7	chr3:105542600-105566000	Weak transcription	Fetal Stomach	stomach
8	chr3:105543400-105560800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:105543400-105581200	Weak transcription	Gastric	stomach
10	chr3:105543800-105571000	Weak transcription	Lung	lung
11	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
13	chr3:105546800-105560800	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:105548400-105561200	Weak transcription	K562	blood
15	chr3:105548400-105561400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:105549000-105560800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:105549000-105571800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:105549200-105564400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:105550000-105562600	Weak transcription	HUVEC	blood vessel
20	chr3:105550000-105569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:105551800-105560800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:105553400-105564000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:105554000-105566400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:105555000-105561400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:105555000-105562800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:105555000-105562800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:105555200-105561200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:105555200-105566400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:105555800-105564400	Weak transcription	HMEC	breast
30	chr3:105555800-105565800	Weak transcription	Right Atrium	heart
31	chr3:105555800-105576600	Weak transcription	Psoas Muscle	Psoas
32	chr3:105556200-105560600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:105556200-105560800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:105556200-105561200	Weak transcription	Fetal Brain Male	brain
35	chr3:105556200-105561600	Weak transcription	Brain Substantia Nigra	brain
36	chr3:105556200-105562800	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:105556200-105566600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:105556200-105570200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:105556200-105571600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr3:105556200-105579000	Weak transcription	Stomach Mucosa	stomach
41	chr3:105556400-105560600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:105556400-105560800	Weak transcription	HSMMtube	muscle
43	chr3:105556400-105561000	Weak transcription	Fetal Brain Female	brain
44	chr3:105556400-105562800	Weak transcription	Brain Anterior Caudate	brain
45	chr3:105556400-105562800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:105556400-105562800	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:105556400-105562800	Weak transcription	Fetal Kidney	kidney
48	chr3:105556400-105565400	Weak transcription	NHLF	lung
49	chr3:105556400-105565600	Weak transcription	Adipose Nuclei	Adipose
50	chr3:105556400-105566200	Weak transcription	Fetal Heart	heart

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