Variant report

Variant	rs9820060
Chromosome Location	chr3:105546790-105546791
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	chr3:105539575..105542989-chr3:105543009..105546955,3	K562	blood:
2	chr3:105546357..105547931-chr3:105552831..105554477,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12485832	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486371	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487841	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496588	0.90[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2455887	0.86[ASN][1000 genomes]
rs3772512	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56344829	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58882222	0.86[ASN][1000 genomes]
rs6437623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778745	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791765	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793018	1.00[ASN][1000 genomes]
rs6796362	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997629	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997684	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7639888	0.89[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7641825	0.86[YRI][hapmap]
rs7649466	0.88[YRI][hapmap]
rs7650147	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657910	1.00[CHB][hapmap]
rs9841798	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876110	0.89[CEU][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9880744	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
2	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
4	chr3:105521200-105546800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:105528400-105553600	Weak transcription	Fetal Kidney	kidney
6	chr3:105532200-105563000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:105533600-105560600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:105533800-105570000	Weak transcription	Dnd41	blood
9	chr3:105534200-105566200	Weak transcription	Brain Germinal Matrix	brain
10	chr3:105535600-105553800	Weak transcription	Fetal Brain Male	brain
11	chr3:105537800-105546800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:105539400-105551600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:105540800-105569600	Weak transcription	Fetal Thymus	thymus
14	chr3:105541000-105554400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:105541400-105548000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:105541800-105553600	Weak transcription	Fetal Brain Female	brain
17	chr3:105542200-105553600	Weak transcription	Liver	Liver
18	chr3:105542200-105554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:105542400-105548200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:105542600-105548200	Weak transcription	Pancreas	Pancrea
21	chr3:105542600-105555400	Weak transcription	Brain Angular Gyrus	brain
22	chr3:105542600-105566000	Weak transcription	Fetal Stomach	stomach
23	chr3:105542800-105546800	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:105542800-105554400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:105543000-105546800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:105543000-105555600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:105543200-105548400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:105543200-105550200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:105543200-105551600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:105543400-105546800	Weak transcription	Psoas Muscle	Psoas
31	chr3:105543400-105546800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:105543400-105546800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:105543400-105546800	Weak transcription	NHEK	skin
34	chr3:105543400-105548200	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:105543400-105548800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:105543400-105548800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:105543400-105555800	Weak transcription	HepG2	liver
38	chr3:105543400-105560800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:105543400-105581200	Weak transcription	Gastric	stomach
40	chr3:105543600-105546800	Weak transcription	HMEC	breast
41	chr3:105543600-105551000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:105543600-105557200	Weak transcription	Fetal Intestine Large	intestine
43	chr3:105543800-105546800	Weak transcription	Small Intestine	intestine
44	chr3:105543800-105546800	Weak transcription	Hela-S3	cervix
45	chr3:105543800-105548200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:105543800-105549600	Weak transcription	HSMM	muscle
47	chr3:105543800-105551400	Weak transcription	HSMMtube	muscle
48	chr3:105543800-105571000	Weak transcription	Lung	lung
49	chr3:105544000-105547200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:105544000-105548800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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