Variant report

Variant	rs4242778
Chromosome Location	chr10:4918857-4918858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKR1C2-7	chr10:4918829-4919605	NONHSAT011119

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10430753	0.88[ASN][1000 genomes]
rs10751990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078063	0.88[ASN][1000 genomes]
rs10904354	0.88[ASN][1000 genomes]
rs10904355	0.88[ASN][1000 genomes]
rs10904358	0.88[ASN][1000 genomes]
rs10904359	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10904360	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10904362	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs10904364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904367	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10904368	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11252793	0.88[ASN][1000 genomes]
rs11252798	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11252799	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11252800	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11252801	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11252802	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11252803	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11252804	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11252805	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11813511	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1869218	1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs1869221	0.86[ASN][1000 genomes]
rs1901644	0.85[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs1993181	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs2123354	0.86[ASN][1000 genomes]
rs2167703	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2397981	0.84[ASN][1000 genomes]
rs2397984	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2924265	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2924267	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2961568	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2961571	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2961576	0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs2961578	1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs2961586	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2961589	0.88[ASN][1000 genomes]
rs2961591	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2961592	1.00[CHB][hapmap]
rs3110959	0.86[ASN][1000 genomes]
rs34413015	0.88[ASN][1000 genomes]
rs34835589	0.88[ASN][1000 genomes]
rs35710579	0.88[ASN][1000 genomes]
rs3924661	0.82[ASW][hapmap];0.85[CEU][hapmap];0.97[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4242775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242776	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4266965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4295949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4304654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4406725	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4460716	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4478885	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4488090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4520487	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4534472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4540749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4543886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545440	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4551663	0.88[ASN][1000 genomes]
rs4564222	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4880692	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4880693	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4880694	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4880695	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4880696	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4880697	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4880698	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4880699	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4880700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4881366	0.87[AMR][1000 genomes]
rs4881367	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4881368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55708378	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55730798	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55744013	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55909699	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55963870	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56095721	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56259387	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56375548	0.88[ASN][1000 genomes]
rs7067785	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs7069610	0.88[ASN][1000 genomes]
rs7071257	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7076588	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7086904	0.88[ASN][1000 genomes]
rs7089338	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7089546	0.84[CEU][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7092190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7097854	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7894644	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7900145	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7900816	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7906540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7906576	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910207	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7910287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7911527	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7918169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7919113	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7922213	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040343	chr10:4872814-5196815	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540462	chr10:4872814-5196815	Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	esv2762839	chr10:4916614-4928890	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv1042940	chr10:4916614-4974581	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4242778	AKR1E2	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4893000-4925000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:4903400-4924800	Weak transcription	A549	lung
3	chr10:4908800-4944200	Weak transcription	Adipose Nuclei	Adipose
4	chr10:4910200-4920400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr10:4910400-4936400	Weak transcription	Left Ventricle	heart
6	chr10:4914000-4920000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:4914600-4920600	Strong transcription	Liver	Liver
8	chr10:4915400-4919200	Strong transcription	Primary hematopoietic stem cells	blood
9	chr10:4915800-4925000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr10:4915800-4943600	Weak transcription	Aorta	Aorta
11	chr10:4916400-4924600	Weak transcription	K562	blood
12	chr10:4916600-4925000	Weak transcription	Fetal Stomach	stomach
13	chr10:4916800-4936400	Weak transcription	Pancreas	Pancrea
14	chr10:4917600-4925600	Weak transcription	Spleen	Spleen
15	chr10:4917800-4919600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:4918400-4968000	Weak transcription	Primary T cells from cord blood	blood
17	chr10:4918800-4919200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr10:4918800-4931400	Weak transcription	Duodenum Mucosa	Duodenum

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