Variant report

Variant	rs16836940
Chromosome Location	chr1:150416913-150416914
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	chr1:150415565..150418212-chr1:151299345..151301312,2	MCF-7	breast:
2	chr1:150334579..150339410-chr1:150416568..150421026,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163125	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000273481	Chromatin interaction

Extended variants
information (count: 223 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:222)

rs_ID	r²[population]
rs1011546	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1043293	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1050818	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs10788874	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10888581	0.98[EUR][1000 genomes]
rs10888582	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10888584	0.84[YRI][hapmap]
rs11205366	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11205368	0.96[EUR][1000 genomes]
rs11205369	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11205370	0.84[AFR][1000 genomes]
rs11205371	0.82[AFR][1000 genomes]
rs11205375	0.85[AFR][1000 genomes]
rs11205376	0.99[EUR][1000 genomes]
rs11205378	0.99[EUR][1000 genomes]
rs11205380	0.99[EUR][1000 genomes]
rs11205381	0.99[EUR][1000 genomes]
rs11205383	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11580810	0.95[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs11581051	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11581786	0.84[AFR][1000 genomes]
rs11582170	0.98[EUR][1000 genomes]
rs11584488	0.95[EUR][1000 genomes]
rs11584613	0.82[EUR][1000 genomes]
rs11588184	0.93[EUR][1000 genomes]
rs11588185	0.96[EUR][1000 genomes]
rs11588874	0.96[EUR][1000 genomes]
rs11589873	0.95[EUR][1000 genomes]
rs11808242	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11810419	0.88[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap]
rs11811159	0.96[EUR][1000 genomes]
rs11811950	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12097596	0.85[CHD][hapmap]
rs12116970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12120775	0.99[EUR][1000 genomes]
rs12120779	0.99[EUR][1000 genomes]
rs12121133	0.99[EUR][1000 genomes]
rs12121966	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12123103	0.99[EUR][1000 genomes]
rs12126130	0.99[EUR][1000 genomes]
rs12126240	0.99[EUR][1000 genomes]
rs12126327	0.98[EUR][1000 genomes]
rs12126357	0.99[EUR][1000 genomes]
rs12126958	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12128653	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12129037	0.84[ASN][1000 genomes]
rs12129491	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12130082	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12130583	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12131083	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12131672	0.99[EUR][1000 genomes]
rs12132890	0.98[EUR][1000 genomes]
rs12134306	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12136332	0.83[EUR][1000 genomes]
rs12136802	0.97[EUR][1000 genomes]
rs12137967	0.84[EUR][1000 genomes]
rs12139488	0.94[EUR][1000 genomes]
rs12140697	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12141218	0.97[EUR][1000 genomes]
rs12142196	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12144091	0.96[EUR][1000 genomes]
rs12145082	0.96[EUR][1000 genomes]
rs12145566	0.98[EUR][1000 genomes]
rs12145967	0.96[EUR][1000 genomes]
rs1260457	0.88[YRI][hapmap]
rs1262432	0.80[AFR][1000 genomes]
rs12718416	0.89[ASN][1000 genomes]
rs12726415	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs12729719	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12729727	0.93[EUR][1000 genomes]
rs12731296	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs12731738	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12736375	0.84[AFR][1000 genomes]
rs12737757	0.96[EUR][1000 genomes]
rs12738490	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs12739019	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12741448	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12745446	0.96[EUR][1000 genomes]
rs12757823	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13057	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1313568	0.88[YRI][hapmap]
rs13374465	0.80[AFR][1000 genomes]
rs1343965	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1566225	0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs16830437	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16835699	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16835708	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs16835782	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs16835791	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16835911	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16836130	0.83[ASN][1000 genomes]
rs16836139	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16836143	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs16836230	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs16836442	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16836576	0.87[ASN][1000 genomes]
rs16836594	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16836601	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16836786	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16836943	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1694386	0.83[JPT][hapmap]
rs1962480	0.99[EUR][1000 genomes]
rs2015966	0.83[ASN][1000 genomes]
rs2173376	0.90[EUR][1000 genomes]
rs2264417	0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs2275245	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2275778	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2275779	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34029237	0.94[EUR][1000 genomes]
rs34247601	0.96[EUR][1000 genomes]
rs34353365	0.91[EUR][1000 genomes]
rs34391279	0.82[EUR][1000 genomes]
rs34456572	0.98[EUR][1000 genomes]
rs34906632	0.98[EUR][1000 genomes]
rs34933405	0.99[EUR][1000 genomes]
rs35322831	0.98[EUR][1000 genomes]
rs35591746	0.96[EUR][1000 genomes]
rs35699789	0.94[EUR][1000 genomes]
rs35839589	0.90[EUR][1000 genomes]
rs35989785	0.93[EUR][1000 genomes]
rs36020363	0.97[EUR][1000 genomes]
rs36023386	0.83[EUR][1000 genomes]
rs36029278	0.95[EUR][1000 genomes]
rs36038795	0.96[EUR][1000 genomes]
rs36122812	0.95[EUR][1000 genomes]
rs3737319	0.83[ASN][1000 genomes]
rs3806389	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3850841	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3850843	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3850844	0.84[AFR][1000 genomes]
rs3862206	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs41264059	0.96[EUR][1000 genomes]
rs41264139	0.96[EUR][1000 genomes]
rs4926420	0.83[ASN][1000 genomes]
rs4926421	1.00[JPT][hapmap]
rs4926430	0.91[ASN][1000 genomes]
rs4926435	0.87[AFR][1000 genomes]
rs4970922	0.85[LWK][hapmap]
rs4970925	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4970927	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4970946	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970947	0.89[ASN][1000 genomes]
rs4971044	1.00[CHB][hapmap]
rs5011187	0.86[AFR][1000 genomes]
rs522068	0.85[ASN][1000 genomes]
rs55816515	0.98[EUR][1000 genomes]
rs56321241	0.96[EUR][1000 genomes]
rs56882505	0.87[ASN][1000 genomes]
rs56909494	0.87[ASN][1000 genomes]
rs57163995	0.83[ASN][1000 genomes]
rs57272513	0.96[ASN][1000 genomes]
rs57971032	0.96[ASN][1000 genomes]
rs58419446	0.81[ASN][1000 genomes]
rs58516261	0.83[ASN][1000 genomes]
rs59367061	0.87[ASN][1000 genomes]
rs59378360	0.91[ASN][1000 genomes]
rs59639798	0.87[ASN][1000 genomes]
rs59662772	0.96[ASN][1000 genomes]
rs60459288	0.87[ASN][1000 genomes]
rs60531845	0.83[ASN][1000 genomes]
rs60730811	0.83[ASN][1000 genomes]
rs60758881	0.81[ASN][1000 genomes]
rs66513313	0.98[EUR][1000 genomes]
rs6663989	0.81[JPT][hapmap]
rs6670974	0.82[EUR][1000 genomes]
rs6679726	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6680391	0.96[ASN][1000 genomes]
rs6686690	0.96[EUR][1000 genomes]
rs6686809	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6694168	0.99[EUR][1000 genomes]
rs6694394	0.94[EUR][1000 genomes]
rs6700009	0.83[ASN][1000 genomes]
rs6703798	0.97[EUR][1000 genomes]
rs67566205	0.98[EUR][1000 genomes]
rs67654647	0.98[EUR][1000 genomes]
rs67733549	0.83[EUR][1000 genomes]
rs67903303	0.98[EUR][1000 genomes]
rs68097764	0.93[EUR][1000 genomes]
rs696615	0.88[LWK][hapmap];0.88[YRI][hapmap]
rs698921	0.88[LWK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs71622690	0.83[ASN][1000 genomes]
rs71622700	0.99[EUR][1000 genomes]
rs72696844	0.85[EUR][1000 genomes]
rs72696853	0.95[EUR][1000 genomes]
rs72698829	0.98[EUR][1000 genomes]
rs72698868	0.96[EUR][1000 genomes]
rs72698870	0.96[EUR][1000 genomes]
rs73013129	0.83[ASN][1000 genomes]
rs73015063	0.83[ASN][1000 genomes]
rs73015078	0.83[ASN][1000 genomes]
rs73015081	0.83[ASN][1000 genomes]
rs73015095	0.83[ASN][1000 genomes]
rs73015096	0.83[ASN][1000 genomes]
rs73017006	0.83[ASN][1000 genomes]
rs73017073	0.87[ASN][1000 genomes]
rs73017086	0.87[ASN][1000 genomes]
rs73017092	0.91[ASN][1000 genomes]
rs73017102	0.96[ASN][1000 genomes]
rs73019017	0.96[ASN][1000 genomes]
rs73019018	0.96[ASN][1000 genomes]
rs73019020	0.96[ASN][1000 genomes]
rs73019021	0.96[ASN][1000 genomes]
rs73019027	0.96[ASN][1000 genomes]
rs73019028	0.96[ASN][1000 genomes]
rs7411534	0.81[LWK][hapmap]
rs74127616	0.96[EUR][1000 genomes]
rs7417465	0.98[EUR][1000 genomes]
rs7513182	0.84[YRI][hapmap]
rs7519691	0.83[EUR][1000 genomes]
rs7522820	0.83[EUR][1000 genomes]
rs7542068	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs7542510	0.82[EUR][1000 genomes]
rs7552883	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs834225	0.86[LWK][hapmap];0.88[YRI][hapmap]
rs834235	0.88[YRI][hapmap]
rs834237	0.88[YRI][hapmap]
rs871527	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9126	0.80[YRI][hapmap]
rs9436009	0.84[YRI][hapmap]
rs953127	0.89[ASN][1000 genomes]
rs9651184	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9661040	0.81[LWK][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16836940	MRPS21	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150373200-150442800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:150380600-150429800	Weak transcription	Aorta	Aorta
3	chr1:150381800-150417400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:150382000-150418200	Weak transcription	Colonic Mucosa	Colon
5	chr1:150382000-150432400	Weak transcription	Fetal Brain Male	brain
6	chr1:150383400-150419000	Weak transcription	Fetal Kidney	kidney
7	chr1:150383400-150419000	Weak transcription	Gastric	stomach
8	chr1:150383400-150432200	Weak transcription	Right Ventricle	heart
9	chr1:150383400-150443200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:150383600-150418200	Weak transcription	Pancreas	Pancrea
11	chr1:150386800-150429800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:150389400-150423400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:150389600-150417000	Weak transcription	HMEC	breast
14	chr1:150390000-150429600	Weak transcription	A549	lung
15	chr1:150392600-150418400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:150393200-150418200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:150393400-150429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:150393600-150418800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:150393600-150420600	Weak transcription	Brain Angular Gyrus	brain
20	chr1:150393600-150429800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:150393800-150429800	Weak transcription	NHEK	skin
22	chr1:150395800-150419000	Weak transcription	Spleen	Spleen
23	chr1:150397000-150419000	Weak transcription	Esophagus	oesophagus
24	chr1:150401400-150448200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:150405200-150422400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:150405400-150418400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:150406800-150418800	Weak transcription	HSMMtube	muscle
28	chr1:150407800-150418600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:150408400-150425000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:150409600-150427200	Weak transcription	Small Intestine	intestine
31	chr1:150409800-150437000	Strong transcription	Fetal Thymus	thymus
32	chr1:150410000-150429800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:150410800-150434400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:150411000-150429800	Weak transcription	HUVEC	blood vessel
35	chr1:150411200-150446400	Strong transcription	Dnd41	blood
36	chr1:150411600-150422800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:150412000-150443000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:150412600-150428200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:150412800-150417400	Weak transcription	Fetal Intestine Small	intestine
40	chr1:150412800-150417400	Weak transcription	Fetal Stomach	stomach
41	chr1:150412800-150422200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr1:150413000-150421000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:150413200-150422800	Strong transcription	Hela-S3	cervix
44	chr1:150413400-150422400	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr1:150413400-150422600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:150413400-150423800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:150413400-150423800	Strong transcription	Primary B cells from cord blood	blood
48	chr1:150413400-150436000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:150413600-150419200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr1:150413600-150422800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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