Variant report

Variant	rs9816075
Chromosome Location	chr3:51601249-51601250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11720298	0.81[AFR][1000 genomes]
rs12330534	1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13314120	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13316894	1.00[MEX][hapmap]
rs13321674	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];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13325153	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[YRI][hapmap]
rs13327225	1.00[MEX][hapmap]
rs13433729	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17051799	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];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051802	1.00[ASW][hapmap]
rs17051832	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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17081501	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];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28421789	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28452990	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28457212	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28653367	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2883900	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549265	1.00[AMR][1000 genomes]
rs56942057	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59525691	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60823123	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61440245	1.00[ASN][1000 genomes]
rs61737032	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6779163	1.00[MEX][hapmap]
rs6782997	1.00[MEX][hapmap]
rs6806124	1.00[MEX][hapmap]
rs72951441	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951452	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951486	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953413	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953417	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953419	1.00[ASN][1000 genomes]
rs72953421	1.00[ASN][1000 genomes]
rs72953423	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953429	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7627636	1.00[ASN][1000 genomes]
rs904144	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9311470	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9808940	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9809757	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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812008	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812682	1.00[ASN][1000 genomes]
rs9815684	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824779	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];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826664	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827665	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9827917	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9828325	1.00[MEX][hapmap]
rs9838294	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838942	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838994	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839516	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839608	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9840331	1.00[AMR][1000 genomes]
rs9842066	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]
rs9844541	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9846343	1.00[ASN][1000 genomes]
rs9855214	1.00[MEX][hapmap]
rs9855809	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857893	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858497	1.00[AMR][1000 genomes]
rs9864213	1.00[AMR][1000 genomes]
rs9864952	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9866513	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866604	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9870147	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875460	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9878053	1.00[MEX][hapmap]
rs9880050	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]
rs9880909	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881402	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881844	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882601	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990341	0.95[AFR][1000 genomes];1.00[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:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51574000-51615400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:51574000-51624800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:51574200-51616400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:51574400-51613800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:51574600-51601800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:51574600-51624600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:51574800-51624800	Weak transcription	NH-A	brain
8	chr3:51575200-51615600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:51576400-51602000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:51578600-51607000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:51578800-51624400	Weak transcription	Esophagus	oesophagus
12	chr3:51579000-51602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:51579200-51602400	Weak transcription	HMEC	breast
14	chr3:51580000-51602600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:51584200-51602200	Weak transcription	Pancreas	Pancrea
16	chr3:51584200-51602200	Weak transcription	Spleen	Spleen
17	chr3:51584200-51614200	Weak transcription	Aorta	Aorta
18	chr3:51584800-51602200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:51585000-51615600	Weak transcription	NHEK	skin
20	chr3:51585200-51624400	Weak transcription	Brain Germinal Matrix	brain
21	chr3:51585400-51602000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:51585800-51612400	Weak transcription	Fetal Thymus	thymus
23	chr3:51585800-51625000	Weak transcription	Colonic Mucosa	Colon
24	chr3:51586400-51601800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:51587800-51607000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:51587800-51624400	Weak transcription	Hela-S3	cervix
27	chr3:51588000-51612600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:51588000-51640000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:51588200-51612600	Weak transcription	Lung	lung
30	chr3:51589000-51612400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:51589200-51612400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:51590000-51611800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:51590800-51607000	Weak transcription	GM12878-XiMat	blood
34	chr3:51591000-51606800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:51591200-51601600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr3:51591200-51612600	Weak transcription	Thymus	Thymus
37	chr3:51591400-51602200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:51591400-51612200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:51591600-51602200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:51591600-51607000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:51592200-51607000	Weak transcription	Fetal Intestine Large	intestine
42	chr3:51592800-51607200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:51593600-51615600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:51593800-51602000	Weak transcription	Brain Anterior Caudate	brain
45	chr3:51593800-51606800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:51593800-51607000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:51593800-51607000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:51594000-51602600	Weak transcription	NHLF	lung
49	chr3:51594000-51606800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:51594000-51607000	Weak transcription	Fetal Brain Female	brain

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