Variant report

Variant	rs2099892
Chromosome Location	chr3:105557340-105557341
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	chr3:105552724..105554590-chr3:105555325..105557862,2	K562	blood:
2	chr3:105552676..105554224-chr3:105555679..105557862,2	K562	blood:

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

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

rs_ID	r²[population]
rs10804442	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10933833	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711088	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12636287	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13060223	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13085563	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13100446	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1443102	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1470283	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867195	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1992522	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2055557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2399056	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28427229	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28533328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3996189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4447799	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894950	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894953	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894954	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4894957	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894960	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4894962	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6437624	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6788366	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795961	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6807382	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71627856	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7432372	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7637327	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7645021	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7647955	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651784	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769315	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs971110	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9841500	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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:108 , 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	chr3:105544200-105559200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
14	chr3:105546800-105560800	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:105547200-105557400	Weak transcription	Fetal Intestine Small	intestine
16	chr3:105547800-105557400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:105548400-105561200	Weak transcription	K562	blood
18	chr3:105548400-105561400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:105548600-105559600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:105549000-105560800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:105549000-105571800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:105549200-105564400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:105549600-105558000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:105550000-105562600	Weak transcription	HUVEC	blood vessel
25	chr3:105550000-105569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:105551800-105560800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:105553400-105564000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:105553800-105557600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:105554000-105566400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:105555000-105561400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:105555000-105562800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:105555000-105562800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:105555200-105557600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:105555200-105558400	Strong transcription	Placenta	Placenta
35	chr3:105555200-105561200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:105555200-105566400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:105555600-105557400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr3:105555600-105558000	Weak transcription	Spleen	Spleen
39	chr3:105555800-105560000	Weak transcription	Left Ventricle	heart
40	chr3:105555800-105564400	Weak transcription	HMEC	breast
41	chr3:105555800-105565800	Weak transcription	Right Atrium	heart
42	chr3:105555800-105576600	Weak transcription	Psoas Muscle	Psoas
43	chr3:105556200-105558000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:105556200-105559600	Genic enhancers	Osteobl	bone
45	chr3:105556200-105560600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:105556200-105560800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:105556200-105561200	Weak transcription	Fetal Brain Male	brain
48	chr3:105556200-105561600	Weak transcription	Brain Substantia Nigra	brain
49	chr3:105556200-105562800	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:105556200-105566600	Weak transcription	Brain Inferior Temporal Lobe	brain

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