Variant report

Variant	rs13026928
Chromosome Location	chr2:99804278-99804279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99803352..99807235-chr2:99812263..99815669,4	MCF-7	breast:
2	chr2:99796714..99802454-chr2:99802908..99805285,8	K562	blood:
3	chr2:99790005..99792347-chr2:99803607..99805339,2	K562	blood:
4	chr2:99796817..99802176-chr2:99802213..99807656,6	MCF-7	breast:
5	chr2:99795935..99799762-chr2:99803404..99807354,6	MCF-7	breast:
6	chr2:99800478..99805908-chr2:99949969..99953911,6	MCF-7	breast:
7	chr2:99803346..99805828-chr2:99808028..99810018,2	MCF-7	breast:

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

Extended variants
information (count: 123 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1044575	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865029	0.86[EUR][1000 genomes]
rs11123761	0.85[EUR][1000 genomes]
rs11123762	0.86[EUR][1000 genomes]
rs11123763	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11123764	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11123765	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11123766	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11123770	0.85[EUR][1000 genomes]
rs1133977	0.85[EUR][1000 genomes]
rs1133978	0.85[EUR][1000 genomes]
rs11674894	0.83[EUR][1000 genomes]
rs11677247	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11677321	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11678456	0.85[EUR][1000 genomes]
rs11683107	0.85[EUR][1000 genomes]
rs11683188	0.84[EUR][1000 genomes]
rs11684610	0.80[EUR][1000 genomes]
rs11685759	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11688004	0.84[EUR][1000 genomes]
rs11689265	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11692336	0.85[EUR][1000 genomes]
rs11692669	0.81[EUR][1000 genomes]
rs11692699	0.86[EUR][1000 genomes]
rs11693427	0.85[EUR][1000 genomes]
rs11695379	0.86[EUR][1000 genomes]
rs11695751	0.91[EUR][1000 genomes]
rs11883676	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11890338	0.87[EUR][1000 genomes]
rs11895749	0.85[EUR][1000 genomes]
rs11900670	0.86[EUR][1000 genomes]
rs12613624	0.84[EUR][1000 genomes]
rs12619780	0.84[EUR][1000 genomes]
rs12621007	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12987548	0.83[EUR][1000 genomes]
rs12991189	0.81[EUR][1000 genomes]
rs12992218	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12992930	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12995473	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12999417	0.86[EUR][1000 genomes]
rs13000731	0.86[EUR][1000 genomes]
rs13004491	0.84[EUR][1000 genomes]
rs13008171	0.85[EUR][1000 genomes]
rs13009147	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13012481	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13018891	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13020339	0.83[EUR][1000 genomes]
rs13022329	0.86[EUR][1000 genomes]
rs13023479	0.82[AMR][1000 genomes]
rs13023501	0.85[EUR][1000 genomes]
rs13023744	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13030961	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13033012	0.86[EUR][1000 genomes]
rs13035311	0.85[EUR][1000 genomes]
rs13798	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1453563	0.84[EUR][1000 genomes]
rs17759607	0.84[EUR][1000 genomes]
rs2171359	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2171362	0.81[EUR][1000 genomes]
rs2309581	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2516827	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2516828	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2516829	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2516830	0.85[EUR][1000 genomes]
rs2516832	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2516833	0.85[EUR][1000 genomes]
rs2516834	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2516835	0.86[EUR][1000 genomes]
rs2516836	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2632260	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2632261	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2632277	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2632283	0.86[EUR][1000 genomes]
rs2632284	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2964969	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2969379	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34252185	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34272114	0.84[EUR][1000 genomes]
rs34766932	0.84[EUR][1000 genomes]
rs35461437	0.80[EUR][1000 genomes]
rs36071868	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4340581	0.90[EUR][1000 genomes]
rs4347885	0.88[EUR][1000 genomes]
rs4402818	0.85[EUR][1000 genomes]
rs4588238	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4850897	0.85[EUR][1000 genomes]
rs4851187	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4851188	0.85[EUR][1000 genomes]
rs6542863	0.86[EUR][1000 genomes]
rs6542864	0.86[EUR][1000 genomes]
rs6542865	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6542866	0.86[EUR][1000 genomes]
rs6542868	0.87[EUR][1000 genomes]
rs6542869	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6542870	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6708576	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6708878	0.87[EUR][1000 genomes]
rs6712704	0.86[EUR][1000 genomes]
rs6717723	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6717729	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6726618	0.83[EUR][1000 genomes]
rs6727749	0.87[EUR][1000 genomes]
rs6739579	0.86[EUR][1000 genomes]
rs6743355	0.86[EUR][1000 genomes]
rs6751927	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6753063	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6756650	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6757661	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs720228	0.91[EUR][1000 genomes]
rs720229	0.83[EUR][1000 genomes]
rs7349217	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558004	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7572660	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7577477	0.86[EUR][1000 genomes]
rs7584809	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7604557	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7605843	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7608938	0.87[EUR][1000 genomes]
rs8179690	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9941561	0.87[EUR][1000 genomes];0.81[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	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' 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
rs13026928	MITD1	cis	Esophagus Mucosa	GTEx
rs13026928	TSGA10	cis	Esophagus Mucosa	GTEx
rs13026928	TSGA10	cis	lung	GTEx
rs13026928	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs13026928	TSGA10	cis	Thyroid	GTEx
rs13026928	TSGA10	cis	Stomach	GTEx
rs13026928	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs13026928	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs13026928	TSGA10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99798400-99807200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:99798400-99812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:99798600-99804600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:99798600-99805400	Weak transcription	Psoas Muscle	Psoas
5	chr2:99798600-99805600	Weak transcription	Brain Anterior Caudate	brain
6	chr2:99798600-99808000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:99798600-99808200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:99798600-99812000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:99798600-99812000	Weak transcription	Aorta	Aorta
10	chr2:99798600-99814000	Weak transcription	Right Ventricle	heart
11	chr2:99798600-99814800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:99798600-99815200	Weak transcription	Esophagus	oesophagus
13	chr2:99798600-99822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:99798600-99836400	Weak transcription	Small Intestine	intestine
15	chr2:99798800-99804400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:99798800-99804800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:99798800-99805200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:99798800-99805400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:99798800-99805600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:99798800-99805600	Weak transcription	Brain Substantia Nigra	brain
21	chr2:99798800-99805600	Weak transcription	Colonic Mucosa	Colon
22	chr2:99798800-99805600	Weak transcription	Fetal Intestine Large	intestine
23	chr2:99798800-99805600	Weak transcription	NH-A	brain
24	chr2:99798800-99806400	Weak transcription	Thymus	Thymus
25	chr2:99798800-99806600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:99798800-99807800	Weak transcription	NHDF-Ad	bronchial
27	chr2:99798800-99810800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:99798800-99812000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:99798800-99812000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:99798800-99812000	Weak transcription	Fetal Kidney	kidney
31	chr2:99798800-99815400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:99798800-99825600	Weak transcription	Fetal Heart	heart
33	chr2:99799000-99805400	Weak transcription	HSMM	muscle
34	chr2:99799200-99806600	Weak transcription	Brain Germinal Matrix	brain
35	chr2:99799200-99811800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:99799200-99813000	Weak transcription	HUVEC	blood vessel
37	chr2:99799200-99824200	Weak transcription	Fetal Brain Male	brain
38	chr2:99799400-99804600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:99799400-99805400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:99799600-99804600	Weak transcription	Placenta	Placenta
41	chr2:99799600-99805200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:99799600-99805600	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:99799600-99805600	Weak transcription	Fetal Brain Female	brain
44	chr2:99799600-99807200	Weak transcription	Ovary	ovary
45	chr2:99799600-99811200	Weak transcription	HMEC	breast
46	chr2:99799600-99812600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:99799600-99814200	Weak transcription	NHLF	lung
48	chr2:99799800-99805600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:99799800-99805600	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:99799800-99806200	Weak transcription	GM12878-XiMat	blood

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