Variant report

Variant	rs3844242
Chromosome Location	chr1:186465896-186465897
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10798041	0.90[YRI][hapmap]
rs10798051	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10911864	0.91[YRI][hapmap]
rs10911866	0.90[YRI][hapmap]
rs10911869	0.91[AFR][1000 genomes]
rs10911877	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10911878	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10911886	0.80[YRI][hapmap]
rs10911888	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10911890	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10911892	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10911895	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11580808	0.86[EUR][1000 genomes]
rs11582183	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11800651	0.81[ASN][1000 genomes]
rs11801527	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11803944	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs11805124	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11805289	0.86[JPT][hapmap]
rs11806017	0.81[ASN][1000 genomes]
rs11806304	0.86[JPT][hapmap]
rs11809402	0.86[JPT][hapmap]
rs11811320	0.86[JPT][hapmap]
rs11812050	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs12071770	0.84[AFR][1000 genomes]
rs12087470	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12089415	0.92[AFR][1000 genomes]
rs12093901	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12402521	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12404145	0.83[YRI][hapmap]
rs12406189	0.91[AFR][1000 genomes]
rs12406209	0.91[AFR][1000 genomes]
rs12407957	0.90[YRI][hapmap]
rs12409263	0.90[AFR][1000 genomes]
rs12410237	0.91[AFR][1000 genomes]
rs12728706	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12733799	0.86[JPT][hapmap]
rs12740221	0.86[JPT][hapmap]
rs12742751	0.87[JPT][hapmap]
rs12750371	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16825403	0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs16825434	0.82[ASN][1000 genomes]
rs16825469	0.84[AFR][1000 genomes]
rs1799957	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1919194	0.85[JPT][hapmap]
rs1929092	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024761	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2180167	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2207727	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2273774	0.87[JPT][hapmap]
rs2383385	0.92[AFR][1000 genomes]
rs2383508	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33963275	0.81[ASN][1000 genomes]
rs34228564	0.81[ASN][1000 genomes]
rs34396375	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34781399	0.81[ASN][1000 genomes]
rs34869216	0.90[AFR][1000 genomes]
rs35643079	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35868587	0.82[ASN][1000 genomes]
rs35945739	0.81[ASN][1000 genomes]
rs35999012	0.90[AFR][1000 genomes]
rs36105782	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766698	0.86[JPT][hapmap]
rs3766701	0.86[JPT][hapmap]
rs3817586	0.86[JPT][hapmap]
rs3851884	0.91[AFR][1000 genomes]
rs3901243	0.80[ASN][1000 genomes]
rs3901950	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3933210	0.81[ASN][1000 genomes]
rs3934200	0.91[AFR][1000 genomes]
rs4140433	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4567244	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57390268	0.87[AFR][1000 genomes]
rs59547074	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6425035	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6659683	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6666413	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6666813	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6672836	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6674145	0.81[JPT][hapmap]
rs6675505	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6677346	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6679923	0.90[AFR][1000 genomes]
rs6680252	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689065	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6689727	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692629	0.91[AFR][1000 genomes]
rs6694957	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71634164	0.81[ASN][1000 genomes]
rs72719487	0.92[AFR][1000 genomes]
rs72719501	0.84[AFR][1000 genomes]
rs7512750	0.80[YRI][hapmap]
rs7518525	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7523747	0.84[AFR][1000 genomes]
rs7525586	0.89[AFR][1000 genomes]
rs7526069	0.84[AFR][1000 genomes]
rs7534971	0.82[AFR][1000 genomes]
rs7536199	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555973	0.91[AFR][1000 genomes]
rs7556360	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv832059	chr1:186464932-186639125	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186452200-186467800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:186452400-186468400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:186459400-186471800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:186462400-186467200	Weak transcription	NH-A	brain
5	chr1:186462600-186467400	Weak transcription	Stomach Mucosa	stomach
6	chr1:186462600-186469600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:186462800-186467400	Weak transcription	Osteobl	bone
8	chr1:186462800-186467600	Weak transcription	Hela-S3	cervix
9	chr1:186462800-186468000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:186463400-186466000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:186463400-186466000	Weak transcription	Brain Substantia Nigra	brain
12	chr1:186463800-186466200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:186464200-186469600	Weak transcription	Aorta	Aorta
14	chr1:186464400-186466800	Weak transcription	GM12878-XiMat	blood
15	chr1:186464800-186467600	Weak transcription	HMEC	breast
16	chr1:186465000-186467200	Weak transcription	HUVEC	blood vessel
17	chr1:186465000-186467800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:186465200-186467400	Weak transcription	NHEK	skin
19	chr1:186465400-186467600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:186465400-186467600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:186465400-186468000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:186465400-186468600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:186465600-186467000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:186465800-186466800	Weak transcription	A549	lung

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