Variant report

Variant	rs11660814
Chromosome Location	chr18:13425604-13425605
allele	G/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:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:13420820..13426923-chr18:13539560..13544275,11	MCF-7	breast:
2	chr18:13425541..13426168-chr18:13480358..13481275,3	MCF-7	breast:
3	chr18:13423775..13425707-chr18:13529777..13531392,2	MCF-7	breast:
4	chr18:13423652..13426163-chr18:13534292..13536970,2	MCF-7	breast:
5	chr18:13404585..13407254-chr18:13424350..13425888,2	MCF-7	breast:
6	chr18:13420755..13423723-chr18:13423891..13427248,3	MCF-7	breast:
7	chr18:13423647..13426323-chr18:13544588..13547161,2	MCF-7	breast:
8	chr18:13424195..13425764-chr18:13426095..13429086,2	K562	blood:
9	chr18:13425541..13426168-chr18:13480358..13481275,4	MCF-7	breast:
10	chr18:13424152..13426286-chr18:13558464..13561196,2	MCF-7	breast:
11	chr18:13425543..13426414-chr18:13539715..13540443,5	MCF-7	breast:
12	chr18:13394671..13395171-chr18:13425601..13426375,2	MCF-7	breast:
13	chr18:13216337..13220556-chr18:13424361..13428056,10	MCF-7	breast:
14	chr18:13423888..13431259-chr18:13537755..13547044,34	MCF-7	breast:
15	chr18:13423214..13425916-chr18:13457898..13459949,3	MCF-7	breast:
16	chr18:13425598..13426153-chr18:13539806..13540388,2	MCF-7	breast:
17	chr18:13425532..13426465-chr18:13539537..13540631,7	MCF-7	breast:
18	chr18:13215623..13223602-chr18:13421388..13431077,26	MCF-7	breast:
19	chr18:13246207..13249799-chr18:13421227..13425816,5	MCF-7	breast:
20	chr18:13424332..13425932-chr18:13501772..13503738,2	MCF-7	breast:
21	chr18:13425532..13426523-chr18:13539478..13540631,12	MCF-7	breast:
22	chr18:13394668..13395488-chr18:13425518..13426156,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267239	Chromatin interaction
ENSG00000168675	Chromatin interaction
ENSG00000266146	Chromatin interaction
ENSG00000267690	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11080650	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11663519	0.85[JPT][hapmap]
rs11663520	0.85[JPT][hapmap];0.87[YRI][hapmap]
rs7234210	0.85[JPT][hapmap]
rs7239579	0.82[JPT][hapmap]
rs8089195	0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs8093150	0.88[CEU][hapmap];0.89[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	nsv531246	chr18:13298774-14082028	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv909411	chr18:13425604-13493554	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11660814	TXNDC2	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13395000-13426600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr18:13403400-13426400	Weak transcription	Brain Hippocampus Middle	brain
3	chr18:13407600-13427400	Weak transcription	Brain Substantia Nigra	brain
4	chr18:13417200-13427600	Weak transcription	Colon Smooth Muscle	Colon
5	chr18:13417200-13439400	Weak transcription	Fetal Stomach	stomach
6	chr18:13417200-13447200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr18:13417400-13426600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr18:13418200-13426800	Genic enhancers	Fetal Thymus	thymus
9	chr18:13418400-13432000	Weak transcription	Pancreas	Pancrea
10	chr18:13418400-13452200	Weak transcription	Colonic Mucosa	Colon
11	chr18:13418600-13427200	Weak transcription	Fetal Muscle Leg	muscle
12	chr18:13420000-13426600	Weak transcription	Liver	Liver
13	chr18:13421600-13426600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr18:13421600-13435800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr18:13421600-13435800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr18:13421600-13437200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr18:13421600-13446600	Weak transcription	Gastric	stomach
18	chr18:13421800-13426400	Weak transcription	Right Atrium	heart
19	chr18:13422000-13426000	Weak transcription	Right Ventricle	heart
20	chr18:13422400-13428600	Weak transcription	Fetal Heart	heart
21	chr18:13422400-13434400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr18:13422800-13428200	Weak transcription	Adipose Nuclei	Adipose
23	chr18:13423000-13426800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr18:13423000-13427400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr18:13423000-13432200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr18:13424200-13426800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr18:13424200-13429200	Enhancers	Brain Anterior Caudate	brain
28	chr18:13424400-13426800	Enhancers	Dnd41	blood
29	chr18:13424600-13425800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr18:13424600-13426000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr18:13424600-13429200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr18:13425000-13426200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr18:13425000-13436800	Weak transcription	Fetal Brain Female	brain
34	chr18:13425200-13425800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr18:13425200-13426400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr18:13425200-13426400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr18:13425200-13426600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr18:13425400-13425800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr18:13425400-13425800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr18:13425400-13425800	Genic enhancers	Thymus	Thymus
41	chr18:13425400-13426000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr18:13425400-13426200	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr18:13425400-13426600	Enhancers	Duodenum Mucosa	Duodenum
44	chr18:13425400-13426600	Enhancers	Lung	lung
45	chr18:13425400-13426800	Enhancers	Primary T cells fromperipheralblood	blood
46	chr18:13425400-13426800	Enhancers	Stomach Mucosa	stomach
47	chr18:13425400-13427800	Enhancers	Psoas Muscle	Psoas
48	chr18:13425600-13425800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr18:13425600-13425800	Enhancers	Primary T cells from cord blood	blood
50	chr18:13425600-13426200	Enhancers	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links