Variant report

Variant	rs58750544
Chromosome Location	chr1:174352587-174352588
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173991563..173993480-chr1:174352055..174354802,2	K562	blood:

Variant related genes	Relation type
ENSG00000224977	Chromatin interaction

Extended variants
information (count: 185 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:172)

rs_ID	r²[population]
rs1013769	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489255	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10489256	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489258	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489260	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798310	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798311	0.90[ASN][1000 genomes]
rs10798312	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798313	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798314	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10798315	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798319	0.97[ASN][1000 genomes]
rs10912766	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912772	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912774	0.97[ASN][1000 genomes]
rs10912775	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912776	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912777	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10912778	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912779	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912782	0.97[ASN][1000 genomes]
rs10912786	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912789	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912791	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912795	1.00[ASN][1000 genomes]
rs10912799	0.97[ASN][1000 genomes]
rs10912800	0.97[ASN][1000 genomes]
rs10912806	0.89[ASN][1000 genomes]
rs11484645	0.84[ASN][1000 genomes]
rs11487399	0.87[ASN][1000 genomes]
rs11799535	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799704	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807229	0.89[ASN][1000 genomes]
rs11809482	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11810824	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12058377	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059307	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12062170	0.87[ASN][1000 genomes]
rs12062483	0.87[ASN][1000 genomes]
rs12064126	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12064743	0.97[ASN][1000 genomes]
rs12065326	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065454	1.00[ASN][1000 genomes]
rs12069134	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070095	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071794	0.97[ASN][1000 genomes]
rs12073068	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12073751	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074416	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12074754	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076548	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077381	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077529	0.87[ASN][1000 genomes]
rs12078960	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079334	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080407	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081012	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12081046	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12083972	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084291	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084948	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12086693	0.87[ASN][1000 genomes]
rs12090860	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091056	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12092768	0.92[ASN][1000 genomes]
rs12093966	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12095629	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12095679	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12097931	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16828481	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846861	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16846938	0.97[ASN][1000 genomes]
rs16846949	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847012	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806329	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883262	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989177	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012558	0.97[ASN][1000 genomes]
rs2064150	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2072759	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205937	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281009	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281010	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2281011	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860954	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2860955	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860959	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28628056	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2901815	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901817	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901818	0.97[ASN][1000 genomes]
rs2901820	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35425383	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41266050	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233181	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651008	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4651015	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651016	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651019	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652365	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652422	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652425	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652460	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652494	1.00[ASN][1000 genomes]
rs4652500	0.97[ASN][1000 genomes]
rs4652511	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652512	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652513	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5015737	0.97[ASN][1000 genomes]
rs55748748	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56148594	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56200626	0.89[ASN][1000 genomes]
rs56213002	0.97[ASN][1000 genomes]
rs56407387	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57512497	1.00[ASN][1000 genomes]
rs57953555	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60409344	0.89[ASN][1000 genomes]
rs60864659	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61218633	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6656925	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658315	0.97[ASN][1000 genomes]
rs6663959	0.89[ASN][1000 genomes]
rs6668096	0.87[ASN][1000 genomes]
rs6674239	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677262	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681970	0.87[ASN][1000 genomes]
rs6682070	0.87[ASN][1000 genomes]
rs6682997	1.00[ASN][1000 genomes]
rs6684688	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689327	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689589	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6692173	0.87[ASN][1000 genomes]
rs6696945	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6699142	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6699697	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701534	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6701619	0.89[ASN][1000 genomes]
rs6701911	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713532	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72713537	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713540	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713553	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72713583	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713584	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713586	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713591	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713601	0.97[ASN][1000 genomes]
rs72713602	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715204	1.00[ASN][1000 genomes]
rs72715218	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72715224	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72715226	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72715237	0.89[ASN][1000 genomes]
rs74126805	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74128393	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413513	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515116	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517516	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7522253	0.97[ASN][1000 genomes]
rs7535845	0.88[ASN][1000 genomes]
rs7536102	0.97[ASN][1000 genomes]
rs7536987	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7537823	1.00[ASN][1000 genomes]
rs7550472	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7554728	0.80[ASN][1000 genomes]
rs7554740	0.87[ASN][1000 genomes]
rs909533	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs926327	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926349	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969472	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9729907	0.97[ASN][1000 genomes]
rs9730220	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1001803	chr1:174176164-174367747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv872553	chr1:174195629-174373379	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1010069	chr1:174215293-174539512	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv872555	chr1:174343705-174565720	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs58750544	RP11-160H22.5	cis	Thyroid	GTEx
rs58750544	RABGAP1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174298000-174361800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:174310600-174362400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:174315600-174366400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:174318800-174369800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:174319200-174362600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:174322400-174363000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:174325800-174382800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:174327400-174362000	Weak transcription	Primary T cells from cord blood	blood
9	chr1:174327600-174362200	Weak transcription	Aorta	Aorta
10	chr1:174328800-174366400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:174334800-174361800	Weak transcription	Left Ventricle	heart
12	chr1:174335000-174361800	Weak transcription	Primary B cells from cord blood	blood
13	chr1:174341200-174353400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:174341800-174372200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:174343000-174362200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:174344000-174362200	Weak transcription	GM12878-XiMat	blood
17	chr1:174346800-174362200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:174351000-174369000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:174352000-174366000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:174352200-174366400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:174352400-174353000	Active TSS	H9 Cell Line	embryonic stem cell

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