Variant report

Variant	rs13399762
Chromosome Location	chr2:55880308-55880309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10172181	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10172506	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10173150	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182131	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10194634	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10195281	0.88[AMR][1000 genomes]
rs10200159	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10203953	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10204169	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045920	0.94[AMR][1000 genomes]
rs10496044	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676573	0.82[ASN][1000 genomes]
rs11902712	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12615063	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12616982	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12622830	0.94[ASN][1000 genomes]
rs12623625	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs13382187	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13383352	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13400946	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13403782	0.87[AFR][1000 genomes]
rs13407344	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13420929	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs13428382	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13428486	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13430684	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17047094	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17047119	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2867964	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs3748955	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6545507	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6545508	0.82[ASN][1000 genomes]
rs6545509	0.82[ASN][1000 genomes]
rs6545510	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6545512	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6545513	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6705295	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6712314	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6717574	0.83[AMR][1000 genomes]
rs6725101	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736996	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6739788	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6760959	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7558127	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7567115	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7571482	0.85[AFR][1000 genomes]
rs7575906	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7582174	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7584120	0.81[AFR][1000 genomes]
rs7586115	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7586124	0.94[AMR][1000 genomes]
rs7586366	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7594212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594497	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9309267	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9309268	0.94[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv9791	chr2:55872725-55883751	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
4	chr2:55849800-55882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:55853600-55882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
7	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
8	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:55864200-55882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:55864400-55919600	Weak transcription	NHLF	lung
11	chr2:55864600-55881400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:55864600-55881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:55865000-55880400	Weak transcription	HMEC	breast
14	chr2:55866200-55882400	Weak transcription	Ovary	ovary
15	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:55870400-55887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:55870400-55887800	Weak transcription	Fetal Brain Female	brain
18	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:55870600-55881400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:55870600-55892800	Weak transcription	Psoas Muscle	Psoas
21	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:55870800-55888000	Weak transcription	Colonic Mucosa	Colon
23	chr2:55870800-55893400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:55870800-55903600	Weak transcription	Gastric	stomach
25	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
27	chr2:55871000-55880600	Weak transcription	Lung	lung
28	chr2:55871000-55887800	Weak transcription	Esophagus	oesophagus
29	chr2:55871000-55893200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:55871000-55893200	Weak transcription	Thymus	Thymus
31	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
32	chr2:55871200-55880400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:55871200-55880600	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:55871200-55893400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
36	chr2:55871400-55882600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:55871400-55905200	Weak transcription	Fetal Kidney	kidney
38	chr2:55873000-55888400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr2:55873200-55881000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:55873200-55893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
42	chr2:55873800-55882600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:55873800-55899400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:55874000-55880600	Weak transcription	GM12878-XiMat	blood
45	chr2:55874200-55881400	Weak transcription	NHDF-Ad	bronchial
46	chr2:55874800-55880400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
48	chr2:55875000-55880600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:55875200-55880600	Weak transcription	Placenta	Placenta
50	chr2:55875600-55880400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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