Variant report

Variant	rs60613973
Chromosome Location	chr12:50058261-50058262
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50055936..50058449-chr12:50062400..50065896,4	K562	blood:
2	chr12:50057650..50059736-chr12:50100384..50101939,2	K562	blood:
3	chr12:50027133..50028767-chr12:50057357..50059815,2	K562	blood:
4	chr12:50054459..50059214-chr12:50133848..50137587,7	K562	blood:
5	chr12:50046427..50048004-chr12:50057517..50059329,2	MCF-7	breast:
6	chr12:50057880..50060234-chr21:47402833..47404920,2	MCF-7	breast:
7	chr12:50054340..50058502-chr12:50061913..50069673,7	K562	blood:

Variant related genes	Relation type
ENSG00000139644	Chromatin interaction
ENSG00000161791	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1012874	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506287	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506288	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169126	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169143	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169145	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830696	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11836837	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837639	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306422	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306430	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306481	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307828	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313354	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315524	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317778	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1317131	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123764	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17123927	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123970	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993398	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336447	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4641552	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55637397	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56737983	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56743994	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56906356	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56945609	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57291131	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58756176	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59261129	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60094911	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60126713	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60415769	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61281663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298080	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74086906	0.83[AFR][1000 genomes]
rs74086911	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087113	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087134	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087188	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs74089557	0.86[ASN][1000 genomes]
rs74089564	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74089566	1.00[ASN][1000 genomes]
rs74089570	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089573	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7487779	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7487854	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953412	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964320	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967073	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7968302	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970674	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971176	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971369	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973498	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9805063	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50042400-50067000	Weak transcription	Fetal Brain Male	brain
2	chr12:50052200-50066200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:50052400-50058400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:50052400-50064800	Weak transcription	Fetal Kidney	kidney
5	chr12:50052600-50059200	Weak transcription	Brain Germinal Matrix	brain
6	chr12:50052600-50067000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:50052600-50067400	Weak transcription	Fetal Brain Female	brain
8	chr12:50053600-50060000	Enhancers	Adipose Nuclei	Adipose
9	chr12:50053800-50059200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:50054400-50059000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr12:50054400-50059600	Enhancers	Right Atrium	heart
12	chr12:50054400-50060200	Enhancers	Placenta	Placenta
13	chr12:50054400-50069800	Enhancers	Left Ventricle	heart
14	chr12:50054600-50061000	Genic enhancers	Fetal Muscle Leg	muscle
15	chr12:50055200-50058800	Enhancers	Right Ventricle	heart
16	chr12:50055200-50059800	Enhancers	Fetal Intestine Large	intestine
17	chr12:50055200-50060000	Enhancers	Brain Anterior Caudate	brain
18	chr12:50055200-50060200	Enhancers	Small Intestine	intestine
19	chr12:50055400-50059000	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr12:50055400-50059600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr12:50055400-50060800	Genic enhancers	Fetal Stomach	stomach
22	chr12:50055400-50061400	Enhancers	Brain Substantia Nigra	brain
23	chr12:50055600-50062400	Enhancers	Psoas Muscle	Psoas
24	chr12:50055800-50058400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:50056000-50058600	Enhancers	Colonic Mucosa	Colon
26	chr12:50056000-50058800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr12:50056000-50059000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:50056000-50060000	Enhancers	Liver	Liver
29	chr12:50056200-50058600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:50056200-50059000	Enhancers	NHLF	lung
31	chr12:50056400-50058400	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr12:50056400-50058400	Enhancers	Fetal Muscle Trunk	muscle
33	chr12:50056400-50058800	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr12:50056400-50058800	Enhancers	Hela-S3	cervix
35	chr12:50056400-50059000	Enhancers	HMEC	breast
36	chr12:50056400-50059000	Enhancers	NHDF-Ad	bronchial
37	chr12:50056400-50060000	Enhancers	Brain Cingulate Gyrus	brain
38	chr12:50056600-50058800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:50056600-50058800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:50056600-50059000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:50056800-50058800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:50056800-50059200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:50057000-50059600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:50057000-50060000	Genic enhancers	Fetal Intestine Small	intestine
45	chr12:50057200-50058400	Enhancers	Primary B cells from peripheral blood	blood
46	chr12:50057200-50058800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr12:50057200-50059000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:50057200-50059200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:50057200-50059600	Enhancers	Primary hematopoietic stem cells	blood
50	chr12:50057200-50059600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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