Variant report

Variant	rs12991982
Chromosome Location	chr2:99950797-99950798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99950324..99955285-chr2:100104603..100108030,8	MCF-7	breast:
2	chr2:99800478..99805908-chr2:99949969..99953911,6	MCF-7	breast:
3	chr2:99796308..99800210-chr2:99949212..99956082,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241962	Chromatin interaction
ENSG00000185414	Chromatin interaction
ENSG00000135945	Chromatin interaction
ENSG00000158411	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10179343	0.83[AMR][1000 genomes]
rs11123783	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12162367	0.86[AFR][1000 genomes]
rs12623835	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12992356	0.86[AFR][1000 genomes]
rs13001438	0.83[AMR][1000 genomes]
rs13017843	0.86[AFR][1000 genomes]
rs13028722	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1882598	0.83[AMR][1000 genomes]
rs2309577	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3828162	0.83[AMR][1000 genomes]
rs4850902	0.91[AMR][1000 genomes]
rs4851201	0.84[AFR][1000 genomes]
rs6706425	0.84[AFR][1000 genomes]
rs6712137	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6721031	0.84[AFR][1000 genomes]
rs6726711	0.83[AMR][1000 genomes]
rs72815074	0.83[AMR][1000 genomes]
rs7569805	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7579143	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7599384	0.81[AFR][1000 genomes];0.83[AMR][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	nsv874699	chr2:99898998-100010044	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12991982	TSGA10	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99928200-99951800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:99932000-99951400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:99933600-99950800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:99934800-99952000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:99936800-99951400	Weak transcription	Fetal Heart	heart
6	chr2:99940400-99951600	Weak transcription	Stomach Mucosa	stomach
7	chr2:99941600-99951000	Strong transcription	HSMM	muscle
8	chr2:99943800-99951000	Weak transcription	Fetal Brain Male	brain
9	chr2:99945000-99951600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:99946400-99951600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:99947200-99951600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:99947200-99951800	Weak transcription	Esophagus	oesophagus
13	chr2:99947200-99952000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:99947200-99952000	Weak transcription	Aorta	Aorta
15	chr2:99947200-99952000	Weak transcription	Lung	lung
16	chr2:99947800-99951600	Weak transcription	Colonic Mucosa	Colon
17	chr2:99948400-99950800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:99948400-99951400	Weak transcription	NHLF	lung
19	chr2:99948800-99950800	Genic enhancers	HepG2	liver
20	chr2:99948800-99951600	Weak transcription	Fetal Intestine Small	intestine
21	chr2:99948800-99951600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:99948800-99952000	Weak transcription	Gastric	stomach
23	chr2:99948800-99952000	Weak transcription	Ovary	ovary
24	chr2:99949000-99950800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:99949000-99951600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:99949000-99951600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:99949000-99951600	Weak transcription	Fetal Stomach	stomach
28	chr2:99949000-99951600	Weak transcription	Thymus	Thymus
29	chr2:99949000-99952200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:99949200-99951600	Weak transcription	Brain Anterior Caudate	brain
31	chr2:99949200-99951600	Weak transcription	Brain Substantia Nigra	brain
32	chr2:99949200-99951600	Weak transcription	Fetal Kidney	kidney
33	chr2:99949200-99951600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:99949400-99951400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:99949600-99950800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:99949600-99950800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:99949600-99951000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:99949600-99951200	Weak transcription	Primary B cells from cord blood	blood
39	chr2:99949600-99951400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:99949600-99951400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:99949600-99951400	Weak transcription	NH-A	brain
42	chr2:99949600-99951600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:99949600-99951600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:99949600-99951600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:99949600-99951600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:99949600-99951600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:99949600-99951600	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:99949600-99951600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:99949600-99951600	Weak transcription	HSMMtube	muscle
50	chr2:99949600-99951800	Weak transcription	H9 Cell Line	embryonic stem cell

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