Variant report

Variant	rs2516833
Chromosome Location	chr2:99777405-99777406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99767297..99778137-chr2:99793643..99800044,16	MCF-7	breast:
2	chr2:99777269..99779242-chr2:99790685..99793650,2	K562	blood:
3	chr2:99770248..99774846-chr2:99775390..99781940,16	K562	blood:
4	chr2:99774991..99777436-chr2:99797785..99799967,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158411	Chromatin interaction
ENSG00000241962	Chromatin interaction
ENSG00000185414	Chromatin interaction
ENSG00000273155	Chromatin interaction
ENSG00000135951	Chromatin interaction
ENSG00000144182	Chromatin interaction

Extended variants
information (count: 151 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10167390	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10170063	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10181422	0.81[ASN][1000 genomes]
rs1044575	0.85[EUR][1000 genomes]
rs10865029	0.84[EUR][1000 genomes]
rs11123761	0.83[EUR][1000 genomes]
rs11123762	0.84[EUR][1000 genomes]
rs11123763	0.84[EUR][1000 genomes]
rs11123764	0.84[EUR][1000 genomes]
rs11123765	0.92[EUR][1000 genomes]
rs11123766	0.85[EUR][1000 genomes]
rs11123770	0.95[EUR][1000 genomes]
rs1115756	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1115757	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1133977	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1133978	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11674894	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11677247	0.86[EUR][1000 genomes]
rs11677321	0.80[EUR][1000 genomes]
rs11678456	0.83[EUR][1000 genomes]
rs11683107	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11683188	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11685759	0.91[EUR][1000 genomes]
rs11688004	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11689265	0.91[EUR][1000 genomes]
rs11692336	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11692669	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11692699	0.84[EUR][1000 genomes]
rs11693427	0.84[EUR][1000 genomes]
rs11695379	0.84[EUR][1000 genomes]
rs11695751	0.89[EUR][1000 genomes]
rs11883676	0.85[EUR][1000 genomes]
rs11890338	0.86[EUR][1000 genomes]
rs11895749	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11900670	0.84[EUR][1000 genomes]
rs11903311	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12470471	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12613624	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12619780	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12621007	0.91[EUR][1000 genomes]
rs12987548	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12991189	0.90[EUR][1000 genomes]
rs12992218	0.86[EUR][1000 genomes]
rs12992930	0.85[EUR][1000 genomes]
rs12995473	0.86[EUR][1000 genomes]
rs12999417	0.82[EUR][1000 genomes]
rs13000731	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13004491	0.82[EUR][1000 genomes]
rs13008171	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13009147	0.84[EUR][1000 genomes]
rs13012481	0.84[EUR][1000 genomes]
rs13018891	0.86[EUR][1000 genomes]
rs13022329	0.84[EUR][1000 genomes]
rs13023501	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13023744	0.89[EUR][1000 genomes]
rs13026928	0.85[EUR][1000 genomes]
rs13030961	0.90[EUR][1000 genomes]
rs13031919	0.89[EUR][1000 genomes]
rs13033012	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13035311	0.83[EUR][1000 genomes]
rs13035357	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13407840	0.82[ASN][1000 genomes]
rs13798	0.85[EUR][1000 genomes]
rs1453563	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1453564	0.81[ASN][1000 genomes]
rs1563106	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1563107	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1563108	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17708262	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17759607	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084988	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2171359	0.85[EUR][1000 genomes]
rs2309581	0.85[EUR][1000 genomes]
rs2516827	0.86[EUR][1000 genomes]
rs2516828	0.86[EUR][1000 genomes]
rs2516829	0.86[EUR][1000 genomes]
rs2516830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2516832	0.86[EUR][1000 genomes]
rs2516834	0.90[EUR][1000 genomes]
rs2516835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2516836	0.85[EUR][1000 genomes]
rs2632260	0.92[EUR][1000 genomes]
rs2632261	0.86[EUR][1000 genomes]
rs2632277	0.92[EUR][1000 genomes]
rs2632283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2632284	0.89[EUR][1000 genomes]
rs28648058	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2964969	0.85[EUR][1000 genomes]
rs2969379	0.92[EUR][1000 genomes]
rs34252185	0.89[EUR][1000 genomes]
rs34272114	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34766932	0.82[EUR][1000 genomes]
rs36071868	0.89[EUR][1000 genomes]
rs4340581	0.88[EUR][1000 genomes]
rs4347885	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4402818	0.83[EUR][1000 genomes]
rs4588238	0.83[EUR][1000 genomes]
rs4850897	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851183	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4851187	0.88[EUR][1000 genomes]
rs4851188	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62154638	0.87[ASN][1000 genomes]
rs6542846	0.81[ASN][1000 genomes]
rs6542863	0.84[EUR][1000 genomes]
rs6542864	0.84[EUR][1000 genomes]
rs6542865	0.86[EUR][1000 genomes]
rs6542866	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6542868	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6542869	0.85[EUR][1000 genomes]
rs6542870	0.85[EUR][1000 genomes]
rs6707462	0.82[ASN][1000 genomes]
rs6708576	0.85[EUR][1000 genomes]
rs6708878	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6712704	0.84[EUR][1000 genomes]
rs6717723	0.91[EUR][1000 genomes]
rs6717729	0.85[EUR][1000 genomes]
rs6722164	0.81[ASN][1000 genomes]
rs6724476	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6727749	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6735801	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6737257	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6739579	0.84[EUR][1000 genomes]
rs6740054	0.82[ASN][1000 genomes]
rs6743355	0.84[EUR][1000 genomes]
rs6751927	0.90[EUR][1000 genomes]
rs6753063	0.85[EUR][1000 genomes]
rs6753650	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6754843	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6756650	0.85[EUR][1000 genomes]
rs6757661	0.85[EUR][1000 genomes]
rs720228	0.89[EUR][1000 genomes]
rs720229	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7349217	0.83[EUR][1000 genomes]
rs7558004	0.85[EUR][1000 genomes]
rs7570657	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7571390	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7572660	0.85[EUR][1000 genomes]
rs7577477	0.84[EUR][1000 genomes]
rs7584809	0.84[EUR][1000 genomes]
rs7586608	0.81[ASN][1000 genomes]
rs7591794	0.82[ASN][1000 genomes]
rs7604557	0.90[EUR][1000 genomes]
rs7605734	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7605843	0.85[EUR][1000 genomes]
rs7606635	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7608938	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8179690	0.85[EUR][1000 genomes]
rs9941561	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv535839	chr2:99742621-99793747	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2516833	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs2516833	TSGA10	cis	multi-tissue	Pritchard
rs2516833	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs2516833	TSGA10	cis	lung	GTEx
rs2516833	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs2516833	TSGA10	cis	Esophagus Mucosa	GTEx
rs2516833	TSGA10	cis	Thyroid	GTEx
rs2516833	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs2516833	TSGA10	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99772200-99795600	Weak transcription	Gastric	stomach
2	chr2:99772400-99781600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:99772400-99782000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:99772400-99782800	Weak transcription	Aorta	Aorta
5	chr2:99772400-99784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:99772400-99784000	Weak transcription	Lung	lung
7	chr2:99772400-99784000	Weak transcription	Spleen	Spleen
8	chr2:99772400-99784800	Weak transcription	Pancreas	Pancrea
9	chr2:99772400-99786200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:99772400-99786200	Weak transcription	Psoas Muscle	Psoas
11	chr2:99772400-99795600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:99772400-99795600	Weak transcription	Small Intestine	intestine
13	chr2:99772400-99796400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:99772400-99796600	Weak transcription	Right Ventricle	heart
15	chr2:99772400-99796800	Weak transcription	Colonic Mucosa	Colon
16	chr2:99772400-99797000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:99772600-99778400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:99772600-99778400	Weak transcription	NHDF-Ad	bronchial
19	chr2:99772600-99778800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:99772600-99778800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:99772600-99781800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:99772600-99782200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:99772600-99782200	Weak transcription	HUVEC	blood vessel
24	chr2:99772600-99783600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:99772600-99783600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:99772600-99784000	Weak transcription	Thymus	Thymus
27	chr2:99772600-99784200	Weak transcription	HSMMtube	muscle
28	chr2:99772600-99784400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:99772600-99784800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:99772600-99784800	Weak transcription	NH-A	brain
31	chr2:99772600-99786200	Weak transcription	NHLF	lung
32	chr2:99772600-99795800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:99772600-99796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:99772600-99796600	Weak transcription	Fetal Kidney	kidney
35	chr2:99772600-99797000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:99772800-99779200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:99772800-99781600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:99772800-99781800	Weak transcription	Osteobl	bone
39	chr2:99772800-99782200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:99772800-99782600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:99772800-99783800	Weak transcription	HMEC	breast
42	chr2:99772800-99784000	Weak transcription	A549	lung
43	chr2:99772800-99786000	Weak transcription	Hela-S3	cervix
44	chr2:99772800-99796400	Weak transcription	Fetal Heart	heart
45	chr2:99773000-99781200	Weak transcription	Fetal Thymus	thymus
46	chr2:99773000-99796400	Weak transcription	Fetal Brain Male	brain
47	chr2:99773200-99777600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:99773200-99777800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr2:99773200-99779400	Strong transcription	Adipose Nuclei	Adipose
50	chr2:99773200-99779600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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