Variant report

Variant	rs28536176
Chromosome Location	chr3:113143625-113143626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10511326	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11916690	0.81[EUR][1000 genomes]
rs11921931	0.81[EUR][1000 genomes]
rs13066742	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13083453	0.87[ASN][1000 genomes]
rs13087452	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13098166	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13325046	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1386336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486894	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1486897	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1552432	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1872747	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2087129	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129434	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399479	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28710051	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34049435	0.87[ASN][1000 genomes]
rs35860985	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36054418	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3732803	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3829889	0.81[EUR][1000 genomes]
rs4425226	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4484165	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60279293	0.87[ASN][1000 genomes]
rs6438149	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6438156	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6438157	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6438158	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6438159	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6438161	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66866534	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67211112	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6766615	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6768648	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6768979	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6769516	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6773497	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6778800	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6783965	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6786974	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6787026	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6798938	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6799610	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6808394	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs722392	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7610638	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613546	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7619913	0.81[EUR][1000 genomes]
rs7622740	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7631082	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7631138	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7636128	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869342	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs869343	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9808893	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9814395	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9825827	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9835848	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9836396	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9839921	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9844447	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9851378	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9860549	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9869119	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9872168	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9875025	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113080800-113143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:113099600-113144800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:113102200-113148800	Weak transcription	Brain Angular Gyrus	brain
5	chr3:113102400-113144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:113107200-113145200	Weak transcription	Aorta	Aorta
7	chr3:113109200-113159800	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:113111600-113146400	Weak transcription	Brain Substantia Nigra	brain
9	chr3:113112200-113148400	Weak transcription	Brain Anterior Caudate	brain
10	chr3:113113000-113145600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:113114000-113143800	Weak transcription	Fetal Thymus	thymus
12	chr3:113117600-113148400	Weak transcription	Placenta	Placenta
13	chr3:113119600-113145200	Weak transcription	Lung	lung
14	chr3:113122400-113144800	Weak transcription	Pancreas	Pancrea
15	chr3:113122800-113144000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:113122800-113144000	Weak transcription	Thymus	Thymus
17	chr3:113122800-113144800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:113123000-113144400	Weak transcription	HSMM	muscle
19	chr3:113123200-113143800	Weak transcription	Ovary	ovary
20	chr3:113132600-113146400	Weak transcription	Right Ventricle	heart
21	chr3:113133200-113147800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:113133400-113144600	Weak transcription	NH-A	brain
23	chr3:113134000-113144000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:113134000-113144400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:113134600-113144800	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:113134600-113159800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:113135000-113145600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:113135200-113143800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:113135200-113144000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:113135200-113144200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:113135200-113144800	Weak transcription	Fetal Lung	lung
32	chr3:113135200-113164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:113135400-113143800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:113135400-113143800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:113135400-113143800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:113135400-113143800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:113135400-113144000	Weak transcription	Adipose Nuclei	Adipose
38	chr3:113135400-113144400	Weak transcription	Fetal Kidney	kidney
39	chr3:113135600-113143800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:113135600-113143800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:113136000-113145600	Weak transcription	Fetal Intestine Small	intestine
42	chr3:113136000-113176400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:113136200-113144400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:113136600-113144800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:113136800-113144000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:113137000-113144800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:113137000-113145600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:113137200-113144800	Weak transcription	Gastric	stomach
49	chr3:113137400-113148600	Weak transcription	Small Intestine	intestine
50	chr3:113137400-113160000	Weak transcription	Fetal Stomach	stomach

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