Variant report

Variant	rs2958146
Chromosome Location	chr12:57056025-57056026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57054749..57057054-chr12:57058615..57061624,4	K562	blood:
2	chr12:57051978..57057362-chr12:57059430..57061597,6	K562	blood:
3	chr12:57054945..57056798-chr12:57071104..57072974,2	K562	blood:
4	chr12:57036157..57038877-chr12:57054362..57057150,2	K562	blood:
5	chr12:57055330..57057220-chr12:57057882..57060273,3	MCF-7	breast:
6	chr12:56916195..56918397-chr12:57055172..57057323,2	K562	blood:

Variant related genes	Relation type
ENSG00000110955	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1020848	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747769	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783794	0.83[ASN][1000 genomes]
rs10876913	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876914	1.00[ASN][1000 genomes]
rs10876915	1.00[ASN][1000 genomes]
rs10876916	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1107479	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171914	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171916	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171917	1.00[ASN][1000 genomes]
rs11835120	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837319	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12229457	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465081	1.00[ASN][1000 genomes]
rs1563896	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1563897	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1962963	0.88[ASN][1000 genomes]
rs2255074	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290893	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2926740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950387	0.93[ASN][1000 genomes]
rs2950388	1.00[ASN][1000 genomes]
rs2950390	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950393	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950394	1.00[ASN][1000 genomes]
rs2958123	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958124	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958145	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2958153	0.91[ASN][1000 genomes]
rs2958154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958155	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36012661	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759028	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67046307	1.00[ASN][1000 genomes]
rs7297289	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7303216	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7315472	1.00[ASN][1000 genomes]
rs73337030	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957300	0.80[EUR][1000 genomes]
rs7972420	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7973157	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975783	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7980378	0.94[ASN][1000 genomes]
rs7980835	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs941207	0.94[ASN][1000 genomes]
rs9634246	1.00[ASN][1000 genomes]
rs9634247	0.97[ASN][1000 genomes]
rs9634277	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9989034	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57039800-57059200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:57040400-57056200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:57040400-57059200	Weak transcription	Aorta	Aorta
4	chr12:57040400-57059400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:57040400-57069400	Weak transcription	Right Atrium	heart
6	chr12:57040600-57056400	Weak transcription	Brain Substantia Nigra	brain
7	chr12:57040600-57056400	Weak transcription	Colonic Mucosa	Colon
8	chr12:57040600-57056400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:57040600-57056800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:57040600-57058200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:57040600-57058200	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:57040600-57058800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:57046200-57059400	Weak transcription	Lung	lung
14	chr12:57048800-57056800	Weak transcription	Dnd41	blood
15	chr12:57049400-57056200	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:57049800-57056200	Weak transcription	Left Ventricle	heart
17	chr12:57051400-57056600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:57051400-57056800	Weak transcription	HSMM	muscle
19	chr12:57051400-57057800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:57051400-57058000	Weak transcription	Brain Hippocampus Middle	brain
21	chr12:57051400-57058400	Weak transcription	Brain Angular Gyrus	brain
22	chr12:57051400-57058600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:57051600-57056400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:57052000-57056200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:57052000-57059200	Weak transcription	Spleen	Spleen
26	chr12:57052400-57059200	Weak transcription	NHLF	lung
27	chr12:57052400-57078200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:57052600-57056200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:57052600-57059800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:57053000-57056200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:57053000-57060200	Weak transcription	Right Ventricle	heart
32	chr12:57053200-57056600	Weak transcription	GM12878-XiMat	blood
33	chr12:57053200-57057600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:57053400-57056600	Weak transcription	NH-A	brain
35	chr12:57053600-57056800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:57053800-57056800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:57053800-57056800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:57053800-57056800	Weak transcription	Fetal Kidney	kidney
39	chr12:57054000-57056200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:57054000-57056800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:57054000-57056800	Weak transcription	Brain Anterior Caudate	brain
42	chr12:57054000-57057400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr12:57054000-57059400	Weak transcription	Ovary	ovary
44	chr12:57054200-57064200	Weak transcription	Small Intestine	intestine
45	chr12:57054200-57069600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:57054400-57056200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:57054400-57056200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:57054400-57056400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr12:57054400-57058600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:57054400-57059400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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