Variant report

Variant	rs11692336
Chromosome Location	chr2:99740606-99740607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99740335..99742130-chr2:99742168..99744513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135951	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10167390	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10170063	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10181344	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10181422	0.81[ASN][1000 genomes]
rs1044575	0.84[EUR][1000 genomes]
rs10865029	0.87[EUR][1000 genomes]
rs11123761	0.86[EUR][1000 genomes]
rs11123762	0.87[EUR][1000 genomes]
rs11123763	0.87[EUR][1000 genomes]
rs11123764	0.87[EUR][1000 genomes]
rs11123765	0.91[EUR][1000 genomes]
rs11123766	0.84[EUR][1000 genomes]
rs11123770	0.94[EUR][1000 genomes]
rs1115756	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1115757	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1133977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1133978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11674894	0.91[EUR][1000 genomes]
rs11677247	0.85[EUR][1000 genomes]
rs11678456	0.86[EUR][1000 genomes]
rs11683107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11683188	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685759	0.90[EUR][1000 genomes]
rs11688004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689265	0.89[EUR][1000 genomes]
rs11692669	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11692699	0.87[EUR][1000 genomes]
rs11693427	0.83[EUR][1000 genomes]
rs11695379	0.87[EUR][1000 genomes]
rs11695751	0.92[EUR][1000 genomes]
rs11883676	0.84[EUR][1000 genomes]
rs11890338	0.85[EUR][1000 genomes]
rs11895749	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11900670	0.87[EUR][1000 genomes]
rs11903311	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12470471	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12613624	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619780	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621007	0.89[EUR][1000 genomes]
rs12987548	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12991189	0.89[EUR][1000 genomes]
rs12992218	0.85[EUR][1000 genomes]
rs12992930	0.84[EUR][1000 genomes]
rs12995473	0.85[EUR][1000 genomes]
rs12999417	0.81[EUR][1000 genomes]
rs13000731	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13004491	0.84[EUR][1000 genomes]
rs13008171	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13009147	0.82[EUR][1000 genomes]
rs13012481	0.84[EUR][1000 genomes]
rs13018891	0.85[EUR][1000 genomes]
rs13020339	0.82[EUR][1000 genomes]
rs13022329	0.87[EUR][1000 genomes]
rs13023501	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13023744	0.92[EUR][1000 genomes]
rs13026928	0.85[EUR][1000 genomes]
rs13030961	0.89[EUR][1000 genomes]
rs13031919	0.88[EUR][1000 genomes]
rs13033012	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13035311	0.86[EUR][1000 genomes]
rs13035357	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407840	0.83[ASN][1000 genomes]
rs13798	0.84[EUR][1000 genomes]
rs1453563	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453564	0.82[ASN][1000 genomes]
rs1563106	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1563107	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1563108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17708262	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17759607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084988	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2123686	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2171359	0.84[EUR][1000 genomes]
rs2171362	0.81[EUR][1000 genomes]
rs2309581	0.84[EUR][1000 genomes]
rs2516827	0.85[EUR][1000 genomes]
rs2516828	0.85[EUR][1000 genomes]
rs2516829	0.85[EUR][1000 genomes]
rs2516830	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516832	0.85[EUR][1000 genomes]
rs2516833	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516834	0.88[EUR][1000 genomes]
rs2516835	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516836	0.83[EUR][1000 genomes]
rs2632260	0.91[EUR][1000 genomes]
rs2632261	0.85[EUR][1000 genomes]
rs2632277	0.91[EUR][1000 genomes]
rs2632283	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2632284	0.88[EUR][1000 genomes]
rs28648058	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2964969	0.84[EUR][1000 genomes]
rs2969379	0.91[EUR][1000 genomes]
rs34252185	0.92[EUR][1000 genomes]
rs34272114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34766932	0.85[EUR][1000 genomes]
rs36071868	0.92[EUR][1000 genomes]
rs4340581	0.91[EUR][1000 genomes]
rs4347885	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4374423	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4402818	0.86[EUR][1000 genomes]
rs4588238	0.86[EUR][1000 genomes]
rs4850897	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851183	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4851185	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4851187	0.92[EUR][1000 genomes]
rs4851188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154638	0.91[ASN][1000 genomes]
rs6542846	0.82[ASN][1000 genomes]
rs6542863	0.87[EUR][1000 genomes]
rs6542864	0.87[EUR][1000 genomes]
rs6542865	0.85[EUR][1000 genomes]
rs6542866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542868	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542869	0.84[EUR][1000 genomes]
rs6542870	0.84[EUR][1000 genomes]
rs6707462	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6708576	0.84[EUR][1000 genomes]
rs6708878	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6712704	0.87[EUR][1000 genomes]
rs6717723	0.89[EUR][1000 genomes]
rs6717729	0.84[EUR][1000 genomes]
rs6722164	0.81[ASN][1000 genomes]
rs6724476	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6727749	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6733285	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6735801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6737257	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6739579	0.87[EUR][1000 genomes]
rs6740054	0.83[ASN][1000 genomes]
rs6741773	0.80[EUR][1000 genomes]
rs6743355	0.87[EUR][1000 genomes]
rs6750876	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6751927	0.93[EUR][1000 genomes]
rs6753063	0.84[EUR][1000 genomes]
rs6753650	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6754843	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6756650	0.84[EUR][1000 genomes]
rs6756880	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6757661	0.84[EUR][1000 genomes]
rs720228	0.92[EUR][1000 genomes]
rs720229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7349217	0.82[EUR][1000 genomes]
rs7558004	0.84[EUR][1000 genomes]
rs7570657	0.86[CHB][hapmap];0.80[JPT][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7571390	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7572660	0.84[EUR][1000 genomes]
rs7577477	0.87[EUR][1000 genomes]
rs7584809	0.87[EUR][1000 genomes]
rs7586608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs7588059	0.82[ASN][1000 genomes]
rs7591794	0.83[ASN][1000 genomes]
rs7604557	0.93[EUR][1000 genomes]
rs7605734	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7605843	0.84[EUR][1000 genomes]
rs7606635	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7608938	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8179690	0.84[EUR][1000 genomes]
rs9710648	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9941561	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11692336	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs11692336	TSGA10	cis	lung	GTEx
rs11692336	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs11692336	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs11692336	TSGA10	cis	multi-tissue	Pritchard
rs11692336	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs11692336	TSGA10	cis	Thyroid	GTEx
rs11692336	TSGA10	cis	Whole Blood	GTEx
rs11692336	TSGA10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99729400-99741600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:99735600-99741400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:99736400-99742200	Weak transcription	Pancreas	Pancrea
4	chr2:99738000-99742000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:99738200-99742200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:99738600-99742000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:99738800-99743800	Weak transcription	HepG2	liver
8	chr2:99739200-99741600	Weak transcription	Fetal Kidney	kidney
9	chr2:99739200-99742000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:99739200-99742200	Weak transcription	Small Intestine	intestine
11	chr2:99739200-99746000	Weak transcription	Primary B cells from cord blood	blood
12	chr2:99739400-99741400	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:99739600-99741200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:99739600-99741200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:99739600-99744000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:99739600-99744000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:99739800-99741400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:99739800-99741400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:99739800-99741600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:99739800-99741600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr2:99739800-99742000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:99739800-99742000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:99739800-99742200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:99740200-99740800	ZNF genes & repeats	Primary T cells from cord blood	blood
25	chr2:99740200-99740800	ZNF genes & repeats	Fetal Lung	lung
26	chr2:99740200-99742000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:99740200-99742000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:99740200-99742200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:99740200-99742400	Weak transcription	NHEK	skin
30	chr2:99740400-99741400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:99740400-99741400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:99740400-99741400	Weak transcription	Brain Anterior Caudate	brain
33	chr2:99740400-99742000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:99740400-99742000	Weak transcription	Placenta	Placenta
35	chr2:99740400-99742200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:99740600-99740800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr2:99740600-99740800	Strong transcription	Liver	Liver
38	chr2:99740600-99741800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:99740600-99742200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:99740600-99742200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:99740600-99742200	Weak transcription	Colonic Mucosa	Colon
42	chr2:99740600-99742200	Weak transcription	Thymus	Thymus
43	chr2:99740600-99743000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
44	chr2:99740600-99744000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:99740600-99744400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:99740600-99745000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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