Variant report

Variant	rs11921710
Chromosome Location	chr3:105565615-105565616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD47-8	chr3:105565135-105569968	NONHSAT090970

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1021858	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1021859	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1039544	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10511246	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1075739	0.80[ASN][1000 genomes]
rs11924742	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12633654	0.83[ASN][1000 genomes]
rs12633854	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12635232	0.80[ASN][1000 genomes]
rs12637560	0.88[ASN][1000 genomes]
rs12637809	0.82[ASN][1000 genomes]
rs12639271	0.80[ASN][1000 genomes]
rs1503921	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1561922	0.84[ASN][1000 genomes]
rs16851523	0.80[ASN][1000 genomes]
rs16851539	0.80[ASN][1000 genomes]
rs16851563	0.82[ASN][1000 genomes]
rs16851570	0.82[ASN][1000 genomes]
rs16851587	0.81[ASN][1000 genomes]
rs16851630	0.88[ASN][1000 genomes]
rs1867192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1910499	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1947000	0.82[ASN][1000 genomes]
rs2089091	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2197208	0.82[ASN][1000 genomes]
rs2197209	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4894840	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57520912	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58340800	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59534462	0.88[ASN][1000 genomes]
rs59611997	0.83[ASN][1000 genomes]
rs60619938	0.82[ASN][1000 genomes]
rs6437620	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6437621	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6437626	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6767627	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6804152	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854891	0.84[ASN][1000 genomes]
rs73854894	0.88[ASN][1000 genomes]
rs73857222	0.88[ASN][1000 genomes]
rs7619449	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7624400	0.81[ASN][1000 genomes]
rs7629357	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7634844	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7641825	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7648842	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7649466	0.87[EUR][1000 genomes]
rs9631436	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9657904	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9789988	0.81[ASN][1000 genomes]
rs9826886	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9846534	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9869648	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9874600	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	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
5	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers 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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
2	chr3:105533800-105570000	Weak transcription	Dnd41	blood
3	chr3:105534200-105566200	Weak transcription	Brain Germinal Matrix	brain
4	chr3:105540800-105569600	Weak transcription	Fetal Thymus	thymus
5	chr3:105542600-105566000	Weak transcription	Fetal Stomach	stomach
6	chr3:105543400-105581200	Weak transcription	Gastric	stomach
7	chr3:105543800-105571000	Weak transcription	Lung	lung
8	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
10	chr3:105549000-105571800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:105550000-105569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:105554000-105566400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:105555200-105566400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:105555800-105565800	Weak transcription	Right Atrium	heart
15	chr3:105555800-105576600	Weak transcription	Psoas Muscle	Psoas
16	chr3:105556200-105566600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:105556200-105570200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:105556200-105571600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr3:105556200-105579000	Weak transcription	Stomach Mucosa	stomach
20	chr3:105556400-105566200	Weak transcription	Fetal Heart	heart
21	chr3:105556400-105568000	Weak transcription	HSMM	muscle
22	chr3:105556600-105569600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:105556600-105569800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:105557800-105579200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:105558200-105571800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:105558600-105586600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:105561200-105565800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr3:105561200-105566400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:105561600-105566000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:105561600-105566200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:105561600-105569600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:105561600-105569600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:105561600-105569600	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:105561600-105586200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:105561800-105569800	Weak transcription	HSMMtube	muscle
37	chr3:105562000-105566000	Weak transcription	Placenta	Placenta
38	chr3:105562000-105566400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:105562000-105586000	Weak transcription	K562	blood
40	chr3:105562600-105567000	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr3:105562600-105568400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:105562600-105568800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr3:105562600-105568800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr3:105562800-105566000	Enhancers	Brain Anterior Caudate	brain
45	chr3:105562800-105566400	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr3:105562800-105567200	Enhancers	Brain Hippocampus Middle	brain
47	chr3:105562800-105567400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:105562800-105568200	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:105563000-105567600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:105563000-105569600	Weak transcription	Fetal Muscle Trunk	muscle

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