Variant report

Variant	rs2516828
Chromosome Location	chr2:99772875-99772876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99754528..99760418-chr2:99769364..99773305,11	K562	blood:
2	chr2:99767297..99778137-chr2:99793643..99800044,16	MCF-7	breast:
3	chr2:99769587..99774574-chr2:99795787..99799597,12	MCF-7	breast:
4	chr2:99769128..99773388-chr2:99951603..99955259,4	K562	blood:
5	chr2:99772739..99776053-chr2:99782752..99785644,3	K562	blood:
6	chr2:99770250..99773199-chr2:99783967..99787710,4	MCF-7	breast:
7	chr2:99770887..99773276-chr2:99955255..99957900,2	MCF-7	breast:
8	chr2:99772683..99774239-chr2:99783479..99785071,2	K562	blood:
9	chr2:99755030..99760884-chr2:99769021..99772906,10	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPL30-1	chr2:99772764-99773273	NONHSAT072739

No data

Variant related genes	Relation type
ENSG00000115514	Chromatin interaction
ENSG00000185414	Chromatin interaction
ENSG00000135951	Chromatin interaction
ENSG00000241962	Chromatin interaction
ENSG00000273045	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000158417	Chromatin interaction

Extended variants
information (count: 152 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs10165534	0.87[ASN][1000 genomes]
rs10179043	0.88[ASN][1000 genomes]
rs10196680	0.87[ASN][1000 genomes]
rs1044575	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10865029	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123761	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123762	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123763	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123764	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123765	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123766	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123770	0.83[EUR][1000 genomes]
rs1133977	0.85[EUR][1000 genomes]
rs1133978	0.85[EUR][1000 genomes]
rs11674894	0.80[EUR][1000 genomes]
rs11677247	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677321	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11678456	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11683107	0.86[EUR][1000 genomes]
rs11683188	0.84[EUR][1000 genomes]
rs11684507	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11684610	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11685759	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11688004	0.84[EUR][1000 genomes]
rs11689265	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11692336	0.85[EUR][1000 genomes]
rs11692699	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11693427	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11695379	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11695751	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11883676	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11890338	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11895749	0.85[EUR][1000 genomes]
rs11900670	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12464710	0.84[ASN][1000 genomes]
rs12467679	0.87[ASN][1000 genomes]
rs12473029	0.85[ASN][1000 genomes]
rs12477754	0.87[ASN][1000 genomes]
rs12477978	0.82[ASN][1000 genomes]
rs12613624	0.84[EUR][1000 genomes]
rs12619780	0.84[EUR][1000 genomes]
rs12621007	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12987548	0.83[EUR][1000 genomes]
rs12992218	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992930	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12995473	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999417	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13000731	0.85[EUR][1000 genomes]
rs13004491	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13008171	0.85[EUR][1000 genomes]
rs13008496	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13009147	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13012481	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13018891	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13020339	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13022329	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13023479	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13023501	0.81[EUR][1000 genomes]
rs13023744	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13025880	0.84[AFR][1000 genomes]
rs13026928	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13030961	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13033012	0.85[EUR][1000 genomes]
rs13035311	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1349778	0.87[ASN][1000 genomes]
rs1349779	0.85[ASN][1000 genomes]
rs13798	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1453563	0.84[EUR][1000 genomes]
rs1580068	0.87[ASN][1000 genomes]
rs17708218	0.90[ASN][1000 genomes]
rs17759607	0.84[EUR][1000 genomes]
rs1993230	0.90[ASN][1000 genomes]
rs2045057	0.90[ASN][1000 genomes]
rs2171359	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2171362	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2309524	0.90[ASN][1000 genomes]
rs2309581	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516827	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516829	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516830	0.86[EUR][1000 genomes]
rs2516832	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516833	0.86[EUR][1000 genomes]
rs2516834	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516835	0.87[EUR][1000 genomes]
rs2516836	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2632260	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2632261	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2632277	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2632283	0.87[EUR][1000 genomes]
rs2632284	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964969	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2969379	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34252185	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34272114	0.84[EUR][1000 genomes]
rs34766932	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35461437	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36071868	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4340581	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4347885	0.84[EUR][1000 genomes]
rs4402818	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4588238	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4622780	0.87[ASN][1000 genomes]
rs4850897	0.86[EUR][1000 genomes]
rs4851187	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851188	0.84[EUR][1000 genomes]
rs6542852	0.84[ASN][1000 genomes]
rs6542858	0.87[ASN][1000 genomes]
rs6542863	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542864	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542865	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542866	0.87[EUR][1000 genomes]
rs6542868	0.86[EUR][1000 genomes]
rs6542869	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542870	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6704766	0.87[ASN][1000 genomes]
rs6708576	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6708878	0.86[EUR][1000 genomes]
rs6712704	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6717723	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6717729	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726618	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6727749	0.86[EUR][1000 genomes]
rs6736064	0.87[ASN][1000 genomes]
rs6739579	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6741773	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6743355	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6751927	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6753063	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6753650	0.88[EUR][1000 genomes]
rs6756650	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6757661	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6759354	0.87[ASN][1000 genomes]
rs720228	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs720229	0.83[EUR][1000 genomes]
rs7349217	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7558004	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7558239	0.84[ASN][1000 genomes]
rs7572660	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7577477	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7584809	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7604557	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7605843	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7608938	0.86[EUR][1000 genomes]
rs8179690	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs896886	0.87[ASN][1000 genomes]
rs9308816	0.87[ASN][1000 genomes]
rs972768	0.90[ASN][1000 genomes]
rs9808541	0.82[ASN][1000 genomes]
rs9941561	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2516828	TSGA10	cis	Esophagus Mucosa	GTEx
rs2516828	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs2516828	TSGA10	cis	Thyroid	GTEx
rs2516828	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs2516828	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs2516828	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2516828	MITD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99772200-99795600	Weak transcription	Gastric	stomach
2	chr2:99772400-99773000	Enhancers	Fetal Thymus	thymus
3	chr2:99772400-99773200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:99772400-99773400	Weak transcription	Left Ventricle	heart
5	chr2:99772400-99773600	Enhancers	Primary B cells from peripheral blood	blood
6	chr2:99772400-99775800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:99772400-99775800	Weak transcription	Esophagus	oesophagus
8	chr2:99772400-99776800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:99772400-99777000	Weak transcription	Placenta	Placenta
10	chr2:99772400-99781600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:99772400-99782000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:99772400-99782800	Weak transcription	Aorta	Aorta
13	chr2:99772400-99784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:99772400-99784000	Weak transcription	Lung	lung
15	chr2:99772400-99784000	Weak transcription	Spleen	Spleen
16	chr2:99772400-99784800	Weak transcription	Pancreas	Pancrea
17	chr2:99772400-99786200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:99772400-99786200	Weak transcription	Psoas Muscle	Psoas
19	chr2:99772400-99795600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:99772400-99795600	Weak transcription	Small Intestine	intestine
21	chr2:99772400-99796400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:99772400-99796600	Weak transcription	Right Ventricle	heart
23	chr2:99772400-99796800	Weak transcription	Colonic Mucosa	Colon
24	chr2:99772400-99797000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:99772600-99773000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:99772600-99773000	Enhancers	Fetal Brain Male	brain
27	chr2:99772600-99773000	Enhancers	Fetal Muscle Leg	muscle
28	chr2:99772600-99773000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr2:99772600-99773200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:99772600-99773200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:99772600-99773200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:99772600-99773200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:99772600-99773200	Weak transcription	Adipose Nuclei	Adipose
34	chr2:99772600-99773200	Enhancers	Brain Germinal Matrix	brain
35	chr2:99772600-99773200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:99772600-99773200	Weak transcription	Fetal Lung	lung
37	chr2:99772600-99773200	Weak transcription	HSMM	muscle
38	chr2:99772600-99773400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:99772600-99773400	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr2:99772600-99773400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr2:99772600-99773400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr2:99772600-99773400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr2:99772600-99773400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:99772600-99773400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:99772600-99773400	Weak transcription	Ovary	ovary
46	chr2:99772600-99773600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr2:99772600-99773600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:99772600-99773600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:99772600-99773600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr2:99772600-99773600	Enhancers	Brain Angular Gyrus	brain

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