Variant report

Variant	rs12073068
Chromosome Location	chr1:174333462-174333463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174328732..174330689-chr1:174332303..174334086,2	K562	blood:

Extended variants
information (count: 194 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:181)

rs_ID	r²[population]
rs1013769	0.83[EUR][1000 genomes]
rs10489255	0.93[EUR][1000 genomes]
rs10489256	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10489258	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10489260	0.90[EUR][1000 genomes]
rs10489264	0.81[EUR][1000 genomes]
rs10798310	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10798312	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10798313	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10798314	0.88[EUR][1000 genomes]
rs10798315	0.88[EUR][1000 genomes]
rs10912757	0.82[EUR][1000 genomes]
rs10912758	0.82[EUR][1000 genomes]
rs10912759	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10912762	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10912764	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10912765	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10912766	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10912772	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10912775	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10912776	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10912777	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10912778	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10912779	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10912786	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10912789	0.87[EUR][1000 genomes]
rs10912791	0.87[EUR][1000 genomes]
rs10912795	0.84[EUR][1000 genomes]
rs10912806	0.84[EUR][1000 genomes]
rs1121537	0.84[EUR][1000 genomes]
rs11484645	0.83[EUR][1000 genomes]
rs11799535	0.94[EUR][1000 genomes]
rs11799704	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11801105	0.84[EUR][1000 genomes]
rs11805578	0.80[EUR][1000 genomes]
rs11807229	0.84[EUR][1000 genomes]
rs11809482	0.86[EUR][1000 genomes]
rs11810824	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12058377	0.88[EUR][1000 genomes]
rs12059307	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12060460	0.81[EUR][1000 genomes]
rs12063545	0.82[EUR][1000 genomes]
rs12064126	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12065326	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12065454	0.84[EUR][1000 genomes]
rs12066504	0.82[EUR][1000 genomes]
rs12067852	0.81[EUR][1000 genomes]
rs12069134	0.92[EUR][1000 genomes]
rs12070095	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12073751	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12074107	0.83[EUR][1000 genomes]
rs12074416	0.90[EUR][1000 genomes]
rs12074754	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12076548	0.87[EUR][1000 genomes]
rs12077381	0.90[EUR][1000 genomes]
rs12078960	0.92[EUR][1000 genomes]
rs12079118	0.81[EUR][1000 genomes]
rs12079334	0.87[EUR][1000 genomes]
rs12079879	0.81[EUR][1000 genomes]
rs12080407	0.93[EUR][1000 genomes]
rs12081012	0.86[EUR][1000 genomes]
rs12081046	0.86[EUR][1000 genomes]
rs12083548	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12083814	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12083972	0.90[EUR][1000 genomes]
rs12084291	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12084948	0.86[EUR][1000 genomes]
rs12090860	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12091056	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12091076	0.81[EUR][1000 genomes]
rs12093966	0.86[EUR][1000 genomes]
rs12095629	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12095679	0.86[EUR][1000 genomes]
rs12097252	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12097931	0.92[EUR][1000 genomes]
rs1474575	0.81[EUR][1000 genomes]
rs16828481	0.95[EUR][1000 genomes]
rs16846861	0.93[EUR][1000 genomes]
rs16846949	0.94[EUR][1000 genomes]
rs16847012	0.92[EUR][1000 genomes]
rs1806329	0.92[EUR][1000 genomes]
rs1883262	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1989177	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2064150	0.92[EUR][1000 genomes]
rs2072759	0.86[EUR][1000 genomes]
rs2092084	0.81[EUR][1000 genomes]
rs2142632	0.81[EUR][1000 genomes]
rs2142864	0.82[EUR][1000 genomes]
rs2142865	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2205937	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2281009	0.86[EUR][1000 genomes]
rs2281010	0.86[EUR][1000 genomes]
rs2281011	0.86[EUR][1000 genomes]
rs2860909	0.82[EUR][1000 genomes]
rs2860954	0.93[EUR][1000 genomes]
rs2860955	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2860959	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2861003	0.81[EUR][1000 genomes]
rs28628056	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2901815	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2901817	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2901820	0.85[EUR][1000 genomes]
rs34409674	0.80[EUR][1000 genomes]
rs35425383	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3920486	0.81[EUR][1000 genomes]
rs41266050	0.86[EUR][1000 genomes]
rs4233181	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4651008	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4651015	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4651016	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4651019	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4652365	0.94[EUR][1000 genomes]
rs4652422	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4652425	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4652460	0.88[EUR][1000 genomes]
rs4652494	0.84[EUR][1000 genomes]
rs4652511	0.86[EUR][1000 genomes]
rs4652512	0.86[EUR][1000 genomes]
rs4652513	0.86[EUR][1000 genomes]
rs55748748	0.86[EUR][1000 genomes]
rs56148594	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56200626	0.84[EUR][1000 genomes]
rs56407387	0.85[EUR][1000 genomes]
rs57512497	0.84[EUR][1000 genomes]
rs57953555	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58750544	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60409344	0.80[EUR][1000 genomes]
rs60864659	0.93[EUR][1000 genomes]
rs61218633	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6425278	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6656925	0.88[EUR][1000 genomes]
rs6663959	0.84[EUR][1000 genomes]
rs6665535	0.84[EUR][1000 genomes]
rs6674239	0.88[EUR][1000 genomes]
rs6677262	0.92[EUR][1000 genomes]
rs6678209	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6682070	0.84[EUR][1000 genomes]
rs6682997	0.84[EUR][1000 genomes]
rs6684688	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6689327	0.88[EUR][1000 genomes]
rs6689589	0.85[EUR][1000 genomes]
rs6693198	0.82[EUR][1000 genomes]
rs6696945	0.86[EUR][1000 genomes]
rs6697959	0.82[EUR][1000 genomes]
rs6699142	0.80[EUR][1000 genomes]
rs6699697	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6700482	0.84[EUR][1000 genomes]
rs6701534	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6701619	0.84[EUR][1000 genomes]
rs6701911	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72713528	0.82[EUR][1000 genomes]
rs72713532	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72713537	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72713540	0.94[EUR][1000 genomes]
rs72713553	0.91[EUR][1000 genomes]
rs72713583	0.92[EUR][1000 genomes]
rs72713584	0.92[EUR][1000 genomes]
rs72713586	0.89[EUR][1000 genomes]
rs72713591	0.90[EUR][1000 genomes]
rs72713602	0.86[EUR][1000 genomes]
rs72715204	0.83[EUR][1000 genomes]
rs72715216	0.84[EUR][1000 genomes]
rs72715218	0.86[EUR][1000 genomes]
rs72715224	0.86[EUR][1000 genomes]
rs72715226	0.86[EUR][1000 genomes]
rs72715237	0.84[EUR][1000 genomes]
rs72715240	0.80[EUR][1000 genomes]
rs72715245	0.80[EUR][1000 genomes]
rs74126805	0.92[EUR][1000 genomes]
rs74128393	0.94[EUR][1000 genomes]
rs7413513	0.94[EUR][1000 genomes]
rs7414200	0.81[EUR][1000 genomes]
rs7515116	0.88[EUR][1000 genomes]
rs7517516	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7537823	0.84[EUR][1000 genomes]
rs7550472	0.86[EUR][1000 genomes]
rs7553317	0.84[EUR][1000 genomes]
rs909533	0.85[EUR][1000 genomes]
rs926327	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs926349	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs969472	0.87[EUR][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	esv1795045	chr1:174273004-174346276	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12073068	RP11-160H22.5	cis	Thyroid	GTEx
rs12073068	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs12073068	MRPS14	Cis_1M	lymphoblastoid	RTeQTL
rs12073068	RC3H1	Cis_1M	lymphoblastoid	RTeQTL

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	chr1:174317400-174342400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:174318800-174369800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:174319200-174362600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:174322400-174363000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:174322600-174334000	Weak transcription	Gastric	stomach
9	chr1:174325800-174382800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:174326200-174334000	Weak transcription	Pancreas	Pancrea
11	chr1:174326400-174346800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:174327400-174334000	Weak transcription	Primary B cells from cord blood	blood
13	chr1:174327400-174362000	Weak transcription	Primary T cells from cord blood	blood
14	chr1:174327600-174362200	Weak transcription	Aorta	Aorta
15	chr1:174328600-174343800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:174328600-174345600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:174328800-174347200	Weak transcription	Fetal Intestine Small	intestine
18	chr1:174328800-174366400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:174329200-174333800	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:174332000-174336600	Weak transcription	GM12878-XiMat	blood
21	chr1:174332800-174334000	Weak transcription	Brain Substantia Nigra	brain

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