Variant report

Variant	rs9852251
Chromosome Location	chr3:67472264-67472265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12485908	0.98[ASN][1000 genomes]
rs12495231	0.90[ASN][1000 genomes]
rs13066142	1.00[ASN][1000 genomes]
rs28420787	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4130104	0.98[ASN][1000 genomes]
rs4130105	0.98[ASN][1000 genomes]
rs61603523	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6548532	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6782194	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6807734	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616627	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7620047	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7620816	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7635889	0.86[AFR][1000 genomes]
rs9309789	0.91[AFR][1000 genomes]
rs9815896	0.91[AFR][1000 genomes]
rs9823702	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9823705	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9825584	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826019	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827838	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830906	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833837	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836868	0.88[AFR][1000 genomes]
rs9836975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838227	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843954	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9851352	0.97[ASN][1000 genomes]
rs9851810	0.97[ASN][1000 genomes]
rs9852902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861758	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9865859	0.86[AFR][1000 genomes]
rs9871072	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9878336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878672	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879429	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9882263	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883219	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67420200-67479400	Weak transcription	Esophagus	oesophagus
2	chr3:67425000-67474200	Weak transcription	Gastric	stomach
3	chr3:67435600-67509800	Weak transcription	Ovary	ovary
4	chr3:67435600-67534200	Weak transcription	Aorta	Aorta
5	chr3:67442800-67478000	Weak transcription	Lung	lung
6	chr3:67449400-67486600	Weak transcription	Fetal Stomach	stomach
7	chr3:67451200-67487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:67454600-67478000	Weak transcription	Fetal Intestine Small	intestine
9	chr3:67463000-67487400	Weak transcription	Pancreas	Pancrea
10	chr3:67463200-67478400	Weak transcription	Psoas Muscle	Psoas
11	chr3:67463200-67484200	Weak transcription	Right Ventricle	heart
12	chr3:67465400-67489600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:67466600-67484400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:67466600-67486200	Weak transcription	Left Ventricle	heart
15	chr3:67466600-67508400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:67468600-67472600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:67469200-67475200	Weak transcription	Spleen	Spleen
18	chr3:67469800-67472600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:67470000-67472600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
20	chr3:67470000-67479600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:67470600-67472600	Strong transcription	Primary B cells from cord blood	blood
22	chr3:67470600-67478000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:67470600-67482200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:67471200-67478600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:67471200-67487600	Weak transcription	A549	lung
26	chr3:67471200-67503800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr3:67471400-67474000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:67471400-67475400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:67471400-67475400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:67471400-67497600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:67471600-67472600	Strong transcription	Primary T cells from cord blood	blood
32	chr3:67471600-67473000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:67471600-67474600	Weak transcription	Fetal Heart	heart
34	chr3:67471600-67483400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:67471600-67483800	Weak transcription	Fetal Lung	lung
36	chr3:67471600-67486600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:67471600-67487600	Weak transcription	Fetal Intestine Large	intestine
38	chr3:67471600-67489200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:67471600-67518800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:67471800-67473000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:67471800-67473200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:67471800-67487800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:67472000-67472400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:67472000-67472600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:67472000-67473000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:67472000-67473000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr3:67472000-67473200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:67472000-67475000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:67472000-67482400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:67472000-67506200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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