Variant report

Variant	rs4980890
Chromosome Location	chr12:481950-481951
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1017162	0.89[AMR][1000 genomes]
rs11062212	0.89[AMR][1000 genomes]
rs11062328	0.89[AMR][1000 genomes]
rs11062353	0.89[AMR][1000 genomes]
rs11062355	0.89[AMR][1000 genomes]
rs11062465	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11062616	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11062659	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11834271	0.87[AMR][1000 genomes]
rs12298836	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12301464	0.89[AMR][1000 genomes]
rs12303118	0.89[AMR][1000 genomes]
rs12303378	0.89[AMR][1000 genomes]
rs12304242	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12306188	0.89[AMR][1000 genomes]
rs12312809	0.89[AMR][1000 genomes]
rs12314514	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12315694	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12317640	0.89[AMR][1000 genomes]
rs12317905	0.83[AMR][1000 genomes]
rs12321487	0.85[AMR][1000 genomes]
rs12321513	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12321532	0.85[AMR][1000 genomes]
rs12321546	0.85[AMR][1000 genomes]
rs1541584	0.89[AMR][1000 genomes]
rs16929048	0.85[AMR][1000 genomes]
rs16929851	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2053736	0.81[AMR][1000 genomes]
rs2267987	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2284335	0.89[AMR][1000 genomes]
rs2284336	0.83[AMR][1000 genomes]
rs2300128	0.89[AMR][1000 genomes]
rs2300130	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28880686	0.81[AMR][1000 genomes]
rs3753160	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3759370	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3782854	0.83[AMR][1000 genomes]
rs3815557	0.93[AMR][1000 genomes]
rs4980812	0.93[AMR][1000 genomes]
rs4980870	0.83[AMR][1000 genomes]
rs4980873	0.89[AMR][1000 genomes]
rs4980887	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57139014	0.87[AMR][1000 genomes]
rs57580513	0.87[AMR][1000 genomes]
rs58979246	0.89[AMR][1000 genomes]
rs61349553	0.89[AMR][1000 genomes]
rs720127	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs74057643	0.83[AMR][1000 genomes]
rs74057646	0.83[AMR][1000 genomes]
rs74057651	0.81[AMR][1000 genomes]
rs74057652	0.83[AMR][1000 genomes]
rs74057660	0.83[AMR][1000 genomes]
rs7487555	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7488483	0.81[ASN][1000 genomes]
rs7954487	0.85[AMR][1000 genomes]
rs7970562	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949498	chr12:282465-493900	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1051726	chr12:282465-511843	Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv541304	chr12:282465-635505	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1042991	chr12:282465-666255	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1041574	chr12:282465-812000	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats 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	80 gene(s)	inside rSNPs	diseases
9	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv1050781	chr12:321353-783899	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv1040849	chr12:321619-771493	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv541322	chr12:321619-771493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv1035679	chr12:321619-781558	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv1053519	chr12:321619-828175	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
15	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
16	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
17	nsv898563	chr12:332860-493900	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	esv2757484	chr12:335010-543206	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
19	esv2759875	chr12:335010-990544	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
20	nsv1045638	chr12:349031-893536	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
21	nsv541325	chr12:349031-893536	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
22	nsv1050646	chr12:362398-658665	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
23	nsv541326	chr12:362398-658665	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
24	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
25	nsv898565	chr12:428131-564185	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
26	nsv1052201	chr12:429128-515675	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
27	nsv541328	chr12:429128-515675	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
28	nsv442250	chr12:432808-543847	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	esv2756520	chr12:433151-543206	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
30	nsv1050226	chr12:441032-743195	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
31	nsv1035222	chr12:449993-515675	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
32	esv2758290	chr12:457433-990544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 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	chr12:474600-484600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:474600-492600	Weak transcription	NHEK	skin
3	chr12:474800-484800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:474800-485000	Weak transcription	Esophagus	oesophagus
5	chr12:474800-486200	Weak transcription	Small Intestine	intestine
6	chr12:474800-489000	Weak transcription	Stomach Mucosa	stomach
7	chr12:474800-492800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:474800-495200	Weak transcription	Fetal Heart	heart
9	chr12:475200-484600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:475200-485200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:475200-496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:475400-485200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:475400-486000	Weak transcription	Hela-S3	cervix
14	chr12:476200-482000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:476200-484600	Weak transcription	NH-A	brain
16	chr12:476200-487600	Weak transcription	HMEC	breast
17	chr12:476400-484600	Weak transcription	NHLF	lung
18	chr12:476600-484600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:476800-484400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:476800-484400	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:476800-484600	Weak transcription	Aorta	Aorta
22	chr12:477000-483200	Weak transcription	Fetal Kidney	kidney
23	chr12:477000-484800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:477000-484800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:477000-484800	Weak transcription	Colonic Mucosa	Colon
26	chr12:477000-485000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:477200-484400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:477200-484400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:477200-484600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:477200-485600	Weak transcription	HepG2	liver
31	chr12:477200-485800	Weak transcription	HSMMtube	muscle
32	chr12:477400-484400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:477600-484400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:477600-484600	Weak transcription	Brain Anterior Caudate	brain
35	chr12:477600-486200	Weak transcription	K562	blood
36	chr12:477800-485000	Weak transcription	Right Ventricle	heart
37	chr12:478000-483000	Weak transcription	Fetal Stomach	stomach
38	chr12:478000-484000	Weak transcription	Fetal Intestine Small	intestine
39	chr12:478000-484400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:478000-484400	Weak transcription	Brain Angular Gyrus	brain
41	chr12:478000-484600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:478000-484600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:478000-484600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:478000-484600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr12:478000-484600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:478000-484600	Weak transcription	Lung	lung
47	chr12:478000-484600	Weak transcription	Ovary	ovary
48	chr12:478000-484600	Weak transcription	Psoas Muscle	Psoas
49	chr12:478000-484600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:478000-484600	Weak transcription	Spleen	Spleen

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