Variant report

Variant	rs12746893
Chromosome Location	chr1:93210876-93210877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93209945..93212352-chr1:93296707..93299344,2	K562	blood:
2	chr1:93208801..93211728-chr1:93211944..93214074,2	K562	blood:

Variant related genes	Relation type
ENSG00000122406	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11164803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11164816	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11164820	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs11577426	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11578004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578098	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs11581705	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11583778	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11585590	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs11588545	0.86[AMR][1000 genomes]
rs11589122	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11589660	0.83[EUR][1000 genomes]
rs11591094	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11800409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800771	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs11800848	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs11801763	0.87[YRI][hapmap]
rs11803097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805007	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes]
rs11805229	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11805698	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807962	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11808092	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11809055	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11809700	0.87[EUR][1000 genomes]
rs11810217	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12728322	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12731107	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12733238	0.87[AMR][1000 genomes]
rs12738833	0.94[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs12743005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743520	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12749480	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756698	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12756786	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs1333743	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1415296	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs1854797	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2051841	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2893226	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs34202284	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34221961	0.88[AMR][1000 genomes]
rs34231012	0.91[AMR][1000 genomes]
rs34244251	1.00[CHB][hapmap]
rs34250288	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34288890	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34305407	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34343030	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34734076	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34761380	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34812295	0.89[AMR][1000 genomes]
rs34843292	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35038369	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183060	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35241270	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35311203	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35435370	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35526187	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612297	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35699160	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35705463	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35901796	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36099538	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36114576	0.91[EUR][1000 genomes]
rs3790450	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs4642892	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes]
rs56044027	0.89[AMR][1000 genomes]
rs59864761	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6604026	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs67026262	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67646822	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67876779	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs68160001	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71652503	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724515	0.80[AMR][1000 genomes]
rs72724555	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72724574	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72724586	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724587	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7521417	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	esv1802611	chr1:93090476-93219907	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv997898	chr1:93167128-93228156	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv871263	chr1:93196273-93248228	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12746893	FAM69A	cis	cerebellum	SCAN
rs12746893	EPHX4	cis	parietal	SCAN
rs12746893	HFM1	cis	parietal	SCAN
rs12746893	MYEOV2	trans	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93123600-93213400	Weak transcription	Gastric	stomach
2	chr1:93155800-93213400	Weak transcription	Lung	lung
3	chr1:93186800-93213400	Weak transcription	K562	blood
4	chr1:93189000-93213400	Weak transcription	Fetal Lung	lung
5	chr1:93190000-93221800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:93190200-93220000	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:93191200-93221600	Weak transcription	Fetal Intestine Large	intestine
8	chr1:93192400-93221200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:93192400-93226400	Weak transcription	Esophagus	oesophagus
10	chr1:93193000-93223800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:93193600-93213200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:93194600-93218000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:93195000-93218000	Weak transcription	NHEK	skin
14	chr1:93196200-93213400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:93199600-93211200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:93199600-93211200	Weak transcription	Left Ventricle	heart
17	chr1:93199600-93212800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:93200200-93224000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:93201000-93211000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:93201000-93211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:93201000-93211600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:93201000-93213400	Weak transcription	Adipose Nuclei	Adipose
23	chr1:93201000-93213400	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:93201000-93218200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:93201000-93218200	Weak transcription	NH-A	brain
26	chr1:93201000-93220000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:93205600-93211600	Weak transcription	Small Intestine	intestine
28	chr1:93206000-93213400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:93206200-93211200	Weak transcription	Psoas Muscle	Psoas
30	chr1:93208600-93211000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:93208800-93211600	Weak transcription	Right Atrium	heart
32	chr1:93209200-93213400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:93209200-93222400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:93209200-93227800	Weak transcription	Primary B cells from cord blood	blood
35	chr1:93209400-93213200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:93210000-93218200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:93210000-93221200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:93210400-93211600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:93210400-93212400	Strong transcription	Fetal Intestine Small	intestine
40	chr1:93210600-93211600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:93210600-93211800	Strong transcription	Fetal Stomach	stomach
42	chr1:93210800-93211600	Strong transcription	Placenta	Placenta
43	chr1:93210800-93211600	Strong transcription	Monocytes-CD14+_RO01746	blood

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