Variant report

Variant	rs60092940
Chromosome Location	chr12:42706537-42706538
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42630532..42633088-chr12:42706033..42707534,2	K562	blood:
2	chr12:42706074..42709119-chr12:42717381..42720082,3	K562	blood:
3	chr12:42562862..42565624-chr12:42706310..42708751,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134283	Chromatin interaction
ENSG00000015153	Chromatin interaction
ENSG00000139168	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10160853	0.88[ASN][1000 genomes]
rs1037401	0.89[AMR][1000 genomes]
rs10506175	0.88[ASN][1000 genomes]
rs11181360	0.88[ASN][1000 genomes]
rs11181373	0.88[ASN][1000 genomes]
rs1139095	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11830387	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11832838	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12297206	0.90[ASN][1000 genomes]
rs12300188	0.90[ASN][1000 genomes]
rs12312515	0.88[ASN][1000 genomes]
rs12315471	0.88[ASN][1000 genomes]
rs12317772	0.88[ASN][1000 genomes]
rs12318401	0.88[ASN][1000 genomes]
rs17091061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17091083	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17091094	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17091117	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17091138	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17091141	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17091163	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17091193	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17091220	0.84[AMR][1000 genomes]
rs17091226	0.89[AMR][1000 genomes]
rs17121217	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1962526	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1987127	0.93[ASN][1000 genomes]
rs2305423	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2406676	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2406677	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747559	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810787	0.90[EUR][1000 genomes]
rs3911246	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57447201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57653125	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58594062	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59402225	0.83[EUR][1000 genomes]
rs59423833	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59501472	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59876649	0.85[ASN][1000 genomes]
rs60287587	0.88[ASN][1000 genomes]
rs60598518	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60659836	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73114487	0.88[ASN][1000 genomes]
rs73116432	0.93[ASN][1000 genomes]
rs73116492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73118486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73118500	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73120410	0.83[EUR][1000 genomes]
rs73120468	0.83[EUR][1000 genomes]
rs73120476	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73120499	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73124406	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73124495	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73126404	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73126407	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73126412	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73126433	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73126453	0.95[AMR][1000 genomes]
rs73127418	0.88[ASN][1000 genomes]
rs73127421	0.84[ASN][1000 genomes]
rs73127428	0.86[ASN][1000 genomes]
rs73127435	0.84[ASN][1000 genomes]
rs73131138	0.88[ASN][1000 genomes]
rs7961228	0.90[EUR][1000 genomes];0.93[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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60092940	ZCRB1	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42693600-42719000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:42693800-42708400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:42694000-42706800	Weak transcription	A549	lung
4	chr12:42694000-42707000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:42695200-42710600	Weak transcription	GM12878-XiMat	blood
6	chr12:42695600-42714800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:42696200-42709000	Weak transcription	K562	blood
8	chr12:42696200-42718800	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:42696800-42707000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:42697000-42718800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:42697200-42710600	Weak transcription	Ovary	ovary
12	chr12:42697400-42718000	Weak transcription	HepG2	liver
13	chr12:42698800-42706800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:42699400-42706800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:42699600-42718800	Weak transcription	HUVEC	blood vessel
16	chr12:42699800-42718200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:42700800-42716400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:42701000-42706800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:42701200-42718600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:42701400-42717400	Weak transcription	Pancreas	Pancrea
21	chr12:42701600-42706800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:42701800-42706800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:42701800-42707000	Weak transcription	Fetal Brain Female	brain
24	chr12:42701800-42712200	Weak transcription	Thymus	Thymus
25	chr12:42701800-42718600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:42701800-42718800	Weak transcription	Brain Angular Gyrus	brain
27	chr12:42701800-42719400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:42702000-42706800	Weak transcription	Fetal Thymus	thymus
29	chr12:42702000-42707400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:42702200-42706800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:42702200-42718600	Weak transcription	Brain Substantia Nigra	brain
32	chr12:42702400-42707000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr12:42702400-42714600	Weak transcription	Brain Germinal Matrix	brain
34	chr12:42702600-42706600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:42702600-42706800	Weak transcription	Placenta	Placenta
36	chr12:42702600-42707000	Weak transcription	Primary T cells from cord blood	blood
37	chr12:42702600-42707200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:42702600-42718800	Weak transcription	Colon Smooth Muscle	Colon
39	chr12:42702800-42706800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:42702800-42706800	Weak transcription	Primary B cells from cord blood	blood
41	chr12:42702800-42712200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:42703000-42707000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:42703000-42717400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:42703400-42707400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr12:42703400-42708000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:42703600-42706800	Weak transcription	Fetal Intestine Large	intestine
47	chr12:42703600-42707000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:42703600-42707000	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:42703600-42710200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:42703800-42715000	Weak transcription	Hela-S3	cervix

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