Variant report

Variant	rs3852594
Chromosome Location	chr12:42528784-42528785
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42526307..42530299-chr12:42534078..42537991,4	K562	blood:
2	chr12:42527145..42529069-chr12:42534078..42535824,2	K562	blood:
3	chr12:42528394..42528943-chr4:171498226..171498870,2	MCF-7	breast:
4	chr12:42524054..42526353-chr12:42526883..42528926,2	MCF-7	breast:
5	chr12:42528143..42530319-chr12:42607718..42609289,2	MCF-7	breast:
6	chr12:42526307..42529075-chr12:42536491..42538067,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10492386	0.93[JPT][hapmap];0.83[AMR][1000 genomes]
rs10492387	0.85[JPT][hapmap];0.83[AMR][1000 genomes]
rs10785332	0.80[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs10785336	0.82[AMR][1000 genomes]
rs10880252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880257	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10880263	0.93[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10880274	0.80[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10880276	0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10880285	0.80[GIH][hapmap];0.86[JPT][hapmap]
rs10880286	0.86[LWK][hapmap];0.83[MKK][hapmap];0.84[YRI][hapmap]
rs11181322	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11181325	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181332	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181344	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181347	0.80[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs11181348	0.83[AMR][1000 genomes]
rs11181356	0.80[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11181359	0.80[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs11181383	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11181384	0.93[JPT][hapmap]
rs11181385	0.82[AMR][1000 genomes]
rs11181388	0.80[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs11181426	0.86[JPT][hapmap]
rs11829883	0.82[AMR][1000 genomes]
rs11831168	0.83[AMR][1000 genomes]
rs11832197	0.83[AMR][1000 genomes]
rs12228932	0.83[AMR][1000 genomes]
rs12579560	0.97[GIH][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs12581958	0.91[JPT][hapmap]
rs12582652	0.82[AFR][1000 genomes]
rs12582890	0.80[AMR][1000 genomes]
rs1532220	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17091018	0.80[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs1988893	0.80[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs3810786	0.80[GIH][hapmap];0.86[JPT][hapmap]
rs3810788	0.80[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.84[YRI][hapmap]
rs3810789	0.86[JPT][hapmap]
rs3810790	0.86[JPT][hapmap]
rs3852593	0.82[JPT][hapmap];0.90[MEX][hapmap]
rs60631072	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61940203	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs61940227	0.83[AMR][1000 genomes]
rs61942482	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61942484	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7296847	0.93[GIH][hapmap];0.86[JPT][hapmap]
rs73116436	0.82[AFR][1000 genomes]
rs7485381	0.82[AFR][1000 genomes]
rs7960726	0.80[AFR][1000 genomes]
rs7965273	0.80[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7972986	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7978820	0.83[AMR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3852594	ZCRB1	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42493000-42534400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:42505800-42537000	Weak transcription	Fetal Stomach	stomach
3	chr12:42505800-42537000	Weak transcription	Lung	lung
4	chr12:42512000-42537400	Weak transcription	Ovary	ovary
5	chr12:42512400-42537000	Weak transcription	Placenta	Placenta
6	chr12:42513000-42537000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:42513200-42537200	Weak transcription	Primary T cells from cord blood	blood
8	chr12:42519000-42537000	Weak transcription	Right Atrium	heart
9	chr12:42519200-42529000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:42519200-42537400	Weak transcription	Small Intestine	intestine
11	chr12:42519600-42537200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:42519800-42529000	Weak transcription	GM12878-XiMat	blood
13	chr12:42519800-42536800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:42519800-42537000	Weak transcription	Primary B cells from cord blood	blood
15	chr12:42522600-42537000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:42524000-42537200	Weak transcription	Aorta	Aorta
17	chr12:42524600-42537000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:42524800-42534000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr12:42524800-42537000	Weak transcription	Fetal Kidney	kidney
20	chr12:42524800-42537000	Weak transcription	Gastric	stomach
21	chr12:42524800-42537200	Weak transcription	Left Ventricle	heart
22	chr12:42524800-42537200	Weak transcription	Psoas Muscle	Psoas
23	chr12:42525000-42528800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:42525000-42529000	Weak transcription	Adipose Nuclei	Adipose
25	chr12:42525000-42531600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:42525200-42528800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:42525200-42529400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:42525400-42528800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:42525400-42528800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:42525400-42535800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:42525600-42528800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:42525600-42528800	Weak transcription	NH-A	brain
33	chr12:42525600-42528800	Weak transcription	NHLF	lung
34	chr12:42525600-42534800	Weak transcription	HSMM	muscle
35	chr12:42525600-42536800	Weak transcription	HUVEC	blood vessel
36	chr12:42525800-42528800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:42525800-42528800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:42527800-42531000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:42528000-42529000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:42528200-42530600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:42528400-42529000	Enhancers	Duodenum Mucosa	Duodenum
42	chr12:42528400-42529000	Enhancers	Fetal Intestine Small	intestine
43	chr12:42528400-42529000	Enhancers	NHEK	skin
44	chr12:42528400-42530000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:42528400-42530400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:42528400-42530400	Enhancers	HMEC	breast
47	chr12:42528600-42529200	Genic enhancers	A549	lung
48	chr12:42528600-42529600	Enhancers	Osteobl	bone
49	chr12:42528600-42529800	Enhancers	Muscle Satellite Cultured Cells	--
50	chr12:42528600-42529800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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