Variant report

Variant	rs16860899
Chromosome Location	chr3:113117177-113117178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10934229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10934230	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10934231	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10934233	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs10934234	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11710894	0.81[JPT][hapmap]
rs11717833	0.81[JPT][hapmap]
rs12054036	0.81[EUR][1000 genomes]
rs12629498	0.81[EUR][1000 genomes]
rs12630518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12632492	0.83[EUR][1000 genomes]
rs12634060	0.85[ASN][1000 genomes]
rs12634440	0.80[ASN][1000 genomes]
rs12636959	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637924	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13318454	0.85[ASN][1000 genomes]
rs1463644	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16860850	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16860868	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17882622	0.88[ASN][1000 genomes]
rs2270781	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291413	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2306069	0.83[EUR][1000 genomes]
rs2399481	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs28662393	0.87[ASN][1000 genomes]
rs34965320	0.88[ASN][1000 genomes]
rs3732804	0.80[EUR][1000 genomes]
rs3846046	0.80[JPT][hapmap]
rs3856718	0.81[JPT][hapmap]
rs3856720	0.81[JPT][hapmap]
rs4682133	0.88[ASN][1000 genomes]
rs4682136	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4682137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682485	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682489	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55667700	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55710804	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55748551	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55757335	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55865352	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55973292	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56339567	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60292736	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60329418	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62265992	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62265996	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6438138	0.85[ASN][1000 genomes]
rs6438142	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6801184	0.85[ASN][1000 genomes]
rs6809516	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs73235041	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73235059	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73235065	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73235066	0.87[ASN][1000 genomes]
rs73235068	0.88[ASN][1000 genomes]
rs73237104	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73237110	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237123	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237130	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73237143	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73237146	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73239107	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73239111	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73239117	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73239121	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73239126	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs763805	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7643592	0.86[CHB][hapmap]
rs7643843	0.86[CHB][hapmap]
rs7647220	0.82[CHB][hapmap]
rs7653186	0.82[CHB][hapmap]
rs8179926	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9820386	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9822309	0.88[ASN][1000 genomes]
rs9842039	0.85[ASN][1000 genomes]
rs9844111	0.87[ASN][1000 genomes]
rs9847084	0.85[ASN][1000 genomes]
rs9852204	0.88[ASN][1000 genomes]
rs9857414	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9863193	0.88[ASN][1000 genomes]
rs9878805	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113066400-113117600	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:113072400-113117200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
4	chr3:113080000-113123800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr3:113080200-113117600	Weak transcription	Psoas Muscle	Psoas
6	chr3:113080800-113143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:113081600-113121200	Weak transcription	Ovary	ovary
8	chr3:113081600-113121200	Weak transcription	Pancreas	Pancrea
9	chr3:113090800-113121200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:113092400-113134200	Weak transcription	Fetal Kidney	kidney
11	chr3:113093600-113134800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:113096600-113121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:113097800-113117800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:113098800-113134800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:113099000-113134800	Weak transcription	A549	lung
16	chr3:113099600-113144800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:113101800-113121200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:113102200-113148800	Weak transcription	Brain Angular Gyrus	brain
19	chr3:113102400-113144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:113102800-113122600	Weak transcription	Spleen	Spleen
21	chr3:113103200-113126200	Weak transcription	Right Ventricle	heart
22	chr3:113104000-113117600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:113104000-113127400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:113105200-113122000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:113105600-113124200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:113106800-113117800	Weak transcription	Lung	lung
27	chr3:113106800-113122000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:113106800-113143600	Weak transcription	Dnd41	blood
29	chr3:113107000-113121800	Weak transcription	Fetal Intestine Large	intestine
30	chr3:113107000-113127400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:113107000-113137000	Weak transcription	Esophagus	oesophagus
32	chr3:113107200-113122000	Weak transcription	Gastric	stomach
33	chr3:113107200-113124200	Weak transcription	Fetal Stomach	stomach
34	chr3:113107200-113124200	Weak transcription	GM12878-XiMat	blood
35	chr3:113107200-113124600	Weak transcription	Fetal Intestine Small	intestine
36	chr3:113107200-113145200	Weak transcription	Aorta	Aorta
37	chr3:113107600-113138200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr3:113108600-113125000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:113109400-113121800	Weak transcription	Fetal Lung	lung
41	chr3:113110200-113117800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:113110200-113124400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:113110400-113117600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:113110600-113121200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:113111200-113122000	Weak transcription	HSMM	muscle
46	chr3:113111600-113146400	Weak transcription	Brain Substantia Nigra	brain
47	chr3:113112000-113122200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:113112200-113148400	Weak transcription	Brain Anterior Caudate	brain
49	chr3:113112400-113121400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:113112400-113123200	Strong transcription	Primary T cells from cord blood	blood

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