Variant report

Variant	rs10876978
Chromosome Location	chr12:57769533-57769534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57768640..57770985-chr12:57824479..57826520,2	K562	blood:

Variant related genes	Relation type
ENSG00000258001	Chromatin interaction
ENSG00000179912	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10747777	0.83[AMR][1000 genomes]
rs10747778	0.82[AMR][1000 genomes]
rs10783818	0.80[AMR][1000 genomes]
rs10783819	0.80[AMR][1000 genomes]
rs10783820	0.81[AMR][1000 genomes]
rs10783823	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876976	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10876977	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876980	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876981	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876983	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172165	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172169	0.81[AMR][1000 genomes]
rs11172170	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172177	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172190	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172191	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172205	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172211	0.87[EUR][1000 genomes]
rs11172214	0.83[EUR][1000 genomes]
rs12230111	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12296766	0.81[AMR][1000 genomes]
rs12310220	0.82[AMR][1000 genomes]
rs12423654	0.82[EUR][1000 genomes]
rs12812140	0.81[AMR][1000 genomes]
rs1284252	0.82[EUR][1000 genomes]
rs1798710	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2063778	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28504983	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4075325	0.80[AMR][1000 genomes]
rs4108243	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4760193	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4760228	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760236	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760244	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760305	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760306	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760308	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4760348	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4760356	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760357	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs481196	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs491750	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs492749	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs512223	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs533975	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs537482	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs543410	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs560048	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs568793	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs575153	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581131	0.80[AMR][1000 genomes]
rs6581134	0.85[AMR][1000 genomes]
rs6581135	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6581136	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581139	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7132367	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7133366	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7133939	0.80[AMR][1000 genomes]
rs7135142	0.80[AMR][1000 genomes]
rs7298418	0.84[AMR][1000 genomes]
rs7303070	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7307059	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7309659	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7313824	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7314266	0.82[AMR][1000 genomes]
rs7358684	0.80[AMR][1000 genomes]
rs7398058	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7977908	0.82[AMR][1000 genomes]
rs7980310	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9738004	0.81[EUR][1000 genomes];0.83[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	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv516655	chr12:57763520-57811414	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57694000-57780000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:57695200-57794600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:57704400-57789200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:57722800-57771200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr12:57722800-57786200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:57731400-57789800	Weak transcription	Small Intestine	intestine
7	chr12:57731600-57796000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:57732800-57771800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr12:57734200-57779400	Weak transcription	Spleen	Spleen
10	chr12:57736400-57784200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:57736400-57795000	Weak transcription	Right Ventricle	heart
12	chr12:57736600-57782000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:57736600-57782400	Weak transcription	HSMM	muscle
14	chr12:57736600-57782800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:57740400-57784000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:57741200-57782800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:57742400-57785800	Weak transcription	Fetal Brain Female	brain
18	chr12:57745000-57787800	Weak transcription	Placenta	Placenta
19	chr12:57745400-57772200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:57753200-57823800	Weak transcription	Esophagus	oesophagus
21	chr12:57755800-57770000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr12:57756600-57771000	Weak transcription	K562	blood
23	chr12:57760200-57769800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:57760200-57769800	Weak transcription	Fetal Stomach	stomach
25	chr12:57760400-57769800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:57760400-57775600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:57761000-57775800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:57761200-57779400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:57761200-57787400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:57761400-57769800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:57761400-57772000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:57761400-57778200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:57761400-57778400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:57761400-57780400	Weak transcription	Fetal Muscle Leg	muscle
35	chr12:57761400-57783600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:57761400-57789000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:57761800-57769800	Weak transcription	Primary T cells from cord blood	blood
38	chr12:57762200-57782600	Weak transcription	Hela-S3	cervix
39	chr12:57762400-57778200	Weak transcription	Fetal Kidney	kidney
40	chr12:57762600-57769600	Weak transcription	Primary B cells from cord blood	blood
41	chr12:57762800-57784200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr12:57762800-57784200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:57762800-57811800	Weak transcription	Pancreas	Pancrea
44	chr12:57763000-57782800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:57763000-57796800	Weak transcription	Colonic Mucosa	Colon
46	chr12:57763000-57799200	Weak transcription	Psoas Muscle	Psoas
47	chr12:57763000-57800400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:57763200-57769600	Weak transcription	Liver	Liver
49	chr12:57763200-57769800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:57763400-57785800	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links