Variant report

Variant	rs1246575
Chromosome Location	chr4:75097488-75097489
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10009707	0.84[EUR][1000 genomes]
rs10010575	0.84[TSI][hapmap]
rs10013212	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10017409	0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs10017417	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10018373	0.95[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs10019396	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10023519	0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs10026687	0.83[EUR][1000 genomes]
rs10028285	0.80[EUR][1000 genomes]
rs10433673	0.91[EUR][1000 genomes]
rs10938112	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11724468	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs11731340	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11737662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11945418	0.87[EUR][1000 genomes]
rs1246577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1246578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1246579	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1246580	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1246582	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1246584	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1246586	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1246587	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1246588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1246590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1246591	0.90[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1246594	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs1246597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12500697	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1265327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13116896	0.91[EUR][1000 genomes]
rs13142241	0.88[EUR][1000 genomes]
rs1371796	0.87[EUR][1000 genomes]
rs1371797	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1380561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1460016	0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs1460017	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16850862	0.81[EUR][1000 genomes]
rs17232394	0.83[EUR][1000 genomes]
rs17829765	0.80[TSI][hapmap]
rs1964526	0.90[EUR][1000 genomes]
rs2045616	0.86[TSI][hapmap]
rs2045618	0.87[EUR][1000 genomes]
rs2061508	0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2367555	0.88[EUR][1000 genomes]
rs2367745	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs28378517	0.86[EUR][1000 genomes]
rs28436705	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28539097	0.83[EUR][1000 genomes]
rs28592249	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28644493	0.84[EUR][1000 genomes]
rs28695994	0.92[EUR][1000 genomes]
rs4371587	0.84[EUR][1000 genomes]
rs4502653	0.83[EUR][1000 genomes]
rs4577545	0.81[EUR][1000 genomes]
rs4694184	0.86[EUR][1000 genomes]
rs488440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536541	0.82[EUR][1000 genomes]
rs565831	0.82[EUR][1000 genomes]
rs62312513	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62312515	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62312545	0.83[EUR][1000 genomes]
rs6446983	0.82[EUR][1000 genomes]
rs6446984	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs6446985	0.82[EUR][1000 genomes]
rs6811214	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6814880	0.86[TSI][hapmap]
rs6819605	0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs6821664	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs6835734	0.86[TSI][hapmap]
rs6854203	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6854723	0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs6858809	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7659389	0.84[EUR][1000 genomes]
rs7663269	0.84[TSI][hapmap]
rs7665105	0.84[EUR][1000 genomes]
rs7670535	0.84[EUR][1000 genomes]
rs7672588	0.83[EUR][1000 genomes]
rs7676371	0.82[EUR][1000 genomes]
rs7678292	0.84[EUR][1000 genomes]
rs7681137	1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs7681763	0.82[EUR][1000 genomes]
rs7681912	0.86[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs7683181	0.88[EUR][1000 genomes]
rs9992393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9997322	0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs9997788	0.85[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv594683	chr4:75013441-75106485	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1013260	chr4:75013441-75121643	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1002907	chr4:75013441-75131443	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1004706	chr4:75014770-75121643	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv594684	chr4:75015750-75106485	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1009099	chr4:75089233-75726206	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv967763	chr4:75097295-75098195	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1246575	ANKRD56	cis	parietal	SCAN
rs1246575	CCDC158	cis	parietal	SCAN
rs1246575	CXCL3	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75072200-75099200	Weak transcription	Ovary	ovary
2	chr4:75080600-75109600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:75085400-75102600	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:75086200-75117600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:75090400-75102200	Weak transcription	Pancreas	Pancrea
6	chr4:75091800-75103200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:75093000-75105000	Weak transcription	Lung	lung
8	chr4:75093000-75117400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:75093200-75100600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:75093600-75101000	Weak transcription	Liver	Liver
11	chr4:75095000-75098400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:75096000-75097600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr4:75096200-75097600	Enhancers	NHLF	lung
14	chr4:75096800-75098200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:75097000-75098400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:75097000-75101000	Weak transcription	GM12878-XiMat	blood
17	chr4:75097200-75097600	Enhancers	HSMM	muscle
18	chr4:75097200-75097600	Enhancers	NHEK	skin
19	chr4:75097200-75097800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:75097200-75097800	Enhancers	HUVEC	blood vessel
21	chr4:75097200-75098400	Enhancers	A549	lung
22	chr4:75097400-75097600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:75097400-75097600	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr4:75097400-75098200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:75097400-75098400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:75097400-75098400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr4:75097400-75098400	Enhancers	HSMMtube	muscle
28	chr4:75097400-75098400	Enhancers	NHDF-Ad	bronchial
29	chr4:75097400-75098400	Enhancers	Osteobl	bone
30	chr4:75097400-75099200	Enhancers	Hela-S3	cervix
31	chr4:75097400-75100600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:75097400-75101000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:75097400-75101400	Weak transcription	HMEC	breast
34	chr4:75097400-75117400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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