Variant report

Variant	rs13025880
Chromosome Location	chr2:99807573-99807574
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	chr2:99796817..99802176-chr2:99802213..99807656,6	MCF-7	breast:
2	chr2:99805050..99807613-chr2:99813461..99815531,2	MCF-7	breast:

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

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1044575	0.93[AFR][1000 genomes]
rs11123761	0.84[AFR][1000 genomes]
rs11123764	0.86[AFR][1000 genomes]
rs11677321	0.80[AFR][1000 genomes]
rs11678456	0.80[AFR][1000 genomes]
rs12995473	0.86[AFR][1000 genomes]
rs13035311	0.83[AFR][1000 genomes]
rs13798	0.84[AFR][1000 genomes]
rs2516828	0.84[AFR][1000 genomes]
rs2516829	0.86[AFR][1000 genomes]
rs2632261	0.86[AFR][1000 genomes]
rs34766932	0.83[AFR][1000 genomes]
rs4402818	0.83[AFR][1000 genomes]
rs6542869	0.87[AFR][1000 genomes]
rs6708576	0.92[AFR][1000 genomes]
rs7349217	0.81[AFR][1000 genomes]
rs7558004	0.86[AFR][1000 genomes]
rs7605843	0.84[AFR][1000 genomes]
rs9941561	0.86[AFR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13025880	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs13025880	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs13025880	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs13025880	TSGA10	cis	Thyroid	GTEx
rs13025880	TSGA10	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99798400-99812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:99798600-99808000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:99798600-99808200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:99798600-99812000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:99798600-99812000	Weak transcription	Aorta	Aorta
6	chr2:99798600-99814000	Weak transcription	Right Ventricle	heart
7	chr2:99798600-99814800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:99798600-99815200	Weak transcription	Esophagus	oesophagus
9	chr2:99798600-99822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:99798600-99836400	Weak transcription	Small Intestine	intestine
11	chr2:99798800-99807800	Weak transcription	NHDF-Ad	bronchial
12	chr2:99798800-99810800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:99798800-99812000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:99798800-99812000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:99798800-99812000	Weak transcription	Fetal Kidney	kidney
16	chr2:99798800-99815400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:99798800-99825600	Weak transcription	Fetal Heart	heart
18	chr2:99799200-99811800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:99799200-99813000	Weak transcription	HUVEC	blood vessel
20	chr2:99799200-99824200	Weak transcription	Fetal Brain Male	brain
21	chr2:99799600-99811200	Weak transcription	HMEC	breast
22	chr2:99799600-99812600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:99799600-99814200	Weak transcription	NHLF	lung
24	chr2:99799800-99807800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:99799800-99811000	Weak transcription	Osteobl	bone
26	chr2:99799800-99812000	Weak transcription	Gastric	stomach
27	chr2:99799800-99814400	Weak transcription	Brain Angular Gyrus	brain
28	chr2:99799800-99816800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:99800000-99812000	Weak transcription	Lung	lung
30	chr2:99800400-99808400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:99800400-99816400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:99801000-99808000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:99801600-99808200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:99801600-99812000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:99801600-99812600	Weak transcription	Pancreas	Pancrea
36	chr2:99802600-99807800	Strong transcription	Fetal Stomach	stomach
37	chr2:99802600-99809200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:99802600-99809400	Strong transcription	Liver	Liver
39	chr2:99802600-99817000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:99802800-99809000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr2:99802800-99809000	Strong transcription	Fetal Muscle Leg	muscle
42	chr2:99803000-99809000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:99803000-99809200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:99803000-99814200	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:99803000-99814400	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:99803000-99815200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:99803000-99815800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:99803000-99818400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:99803200-99808200	Strong transcription	Hela-S3	cervix
50	chr2:99803200-99809000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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