Variant report

Variant	rs9808940
Chromosome Location	chr3:51656195-51656196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs12330534	1.00[CHB][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13314120	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13321674	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13325153	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap]
rs13327225	1.00[MEX][hapmap]
rs13433729	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17051799	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes]
rs17051832	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17081501	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28421789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28452990	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28457212	0.85[AMR][1000 genomes]
rs28653367	0.85[AMR][1000 genomes]
rs2883900	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549265	0.85[AMR][1000 genomes]
rs56942057	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59525691	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60823123	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61440245	1.00[ASN][1000 genomes]
rs61737032	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6779163	1.00[MEX][hapmap]
rs6792143	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs6806124	1.00[MEX][hapmap]
rs72951441	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951452	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951472	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951485	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951486	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953413	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953417	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953419	1.00[ASN][1000 genomes]
rs72953421	1.00[ASN][1000 genomes]
rs72953423	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953429	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7627636	1.00[ASN][1000 genomes]
rs904144	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9311470	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9809757	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812008	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812682	1.00[ASN][1000 genomes]
rs9815684	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9816075	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824779	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826664	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827665	0.85[AMR][1000 genomes]
rs9827917	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838294	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838942	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838994	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839516	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839608	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9840331	0.85[AMR][1000 genomes]
rs9842066	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844541	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9846343	1.00[ASN][1000 genomes]
rs9855809	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857893	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858497	0.85[AMR][1000 genomes]
rs9864213	0.85[AMR][1000 genomes]
rs9864952	1.00[ASN][1000 genomes]
rs9866513	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866604	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9870147	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875460	0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9878053	1.00[MEX][hapmap]
rs9878564	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9880050	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880909	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881402	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881844	0.85[AMR][1000 genomes]
rs9882601	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990341	0.81[AFR][1000 genomes];0.85[AMR][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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr3:51625400-51663400	Weak transcription	Right Ventricle	heart
2	chr3:51625600-51658200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:51626000-51656600	Weak transcription	Placenta	Placenta
4	chr3:51628800-51660800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:51630400-51661400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:51630800-51661400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:51631000-51661400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:51631000-51661600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:51631000-51661600	Weak transcription	Fetal Thymus	thymus
10	chr3:51631800-51660800	Weak transcription	Primary B cells from cord blood	blood
11	chr3:51636200-51661200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:51637600-51660800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:51640200-51656400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:51640600-51661000	Weak transcription	Dnd41	blood
15	chr3:51640600-51661200	Weak transcription	Thymus	Thymus
16	chr3:51640600-51663200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:51643000-51660800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:51643600-51656600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:51643800-51661000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:51643800-51661000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:51648800-51656400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:51649800-51663400	Weak transcription	GM12878-XiMat	blood
23	chr3:51650400-51657600	Enhancers	Liver	Liver
24	chr3:51651200-51656200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:51651800-51656800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:51652400-51656600	Enhancers	HepG2	liver
27	chr3:51652600-51657600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr3:51652600-51661000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:51652800-51657600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:51653400-51657400	Enhancers	Stomach Smooth Muscle	stomach
31	chr3:51653600-51656600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr3:51653600-51657600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:51653600-51657600	Enhancers	Colon Smooth Muscle	Colon
34	chr3:51653600-51657600	Enhancers	Rectal Smooth Muscle	rectum
35	chr3:51653800-51657200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:51653800-51657200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:51653800-51657600	Enhancers	NHLF	lung
38	chr3:51654000-51656600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:51654000-51657000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:51654000-51657000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:51654000-51657000	Enhancers	Osteobl	bone
42	chr3:51654000-51657200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr3:51654200-51656400	Weak transcription	Brain Anterior Caudate	brain
44	chr3:51654200-51656600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:51654200-51657000	Enhancers	NHEK	skin
46	chr3:51654200-51661200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:51654600-51656200	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:51654600-51656800	Enhancers	Stomach Mucosa	stomach
49	chr3:51654600-51656800	Enhancers	HMEC	breast
50	chr3:51654600-51657000	Enhancers	HSMM	muscle

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