Variant report

Variant	rs2042743
Chromosome Location	chr18:13427800-13427801
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:13216337..13220556-chr18:13424361..13428056,10	MCF-7	breast:
2	chr18:13423888..13431259-chr18:13537755..13547044,34	MCF-7	breast:
3	chr18:13215623..13223602-chr18:13421388..13431077,26	MCF-7	breast:
4	chr18:13139722..13141913-chr18:13426612..13428353,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267239	Chromatin interaction
ENSG00000168675	Chromatin interaction
ENSG00000267656	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11663519	0.82[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs11663520	0.81[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs11663559	0.85[EUR][1000 genomes]
rs55748182	0.87[EUR][1000 genomes]
rs9959699	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs9960108	0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2042743	TXNDC2	cis	cerebellum	SCAN
rs2042743	PTPN2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13417200-13439400	Weak transcription	Fetal Stomach	stomach
2	chr18:13417200-13447200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr18:13418400-13432000	Weak transcription	Pancreas	Pancrea
4	chr18:13418400-13452200	Weak transcription	Colonic Mucosa	Colon
5	chr18:13421600-13435800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr18:13421600-13435800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr18:13421600-13437200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr18:13421600-13446600	Weak transcription	Gastric	stomach
9	chr18:13422400-13428600	Weak transcription	Fetal Heart	heart
10	chr18:13422400-13434400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr18:13422800-13428200	Weak transcription	Adipose Nuclei	Adipose
12	chr18:13423000-13432200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr18:13424200-13429200	Enhancers	Brain Anterior Caudate	brain
14	chr18:13424600-13429200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr18:13425000-13436800	Weak transcription	Fetal Brain Female	brain
16	chr18:13425400-13427800	Enhancers	Psoas Muscle	Psoas
17	chr18:13425600-13429200	Enhancers	Left Ventricle	heart
18	chr18:13425800-13428200	Strong transcription	Thymus	Thymus
19	chr18:13425800-13435400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr18:13425800-13445200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr18:13426000-13429200	Enhancers	Right Ventricle	heart
22	chr18:13426000-13432600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr18:13426000-13433200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr18:13426200-13428200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:13426200-13428200	Weak transcription	Aorta	Aorta
26	chr18:13426200-13428400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr18:13426200-13428400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr18:13426200-13429200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr18:13426200-13430400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr18:13426200-13439600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr18:13426200-13446200	Weak transcription	Esophagus	oesophagus
32	chr18:13426400-13428000	Enhancers	Brain Hippocampus Middle	brain
33	chr18:13426400-13429200	Enhancers	Right Atrium	heart
34	chr18:13426400-13434800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr18:13426600-13427800	Enhancers	Liver	Liver
36	chr18:13426600-13427800	Enhancers	Brain Cingulate Gyrus	brain
37	chr18:13426600-13428600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr18:13426600-13435000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr18:13426600-13439600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr18:13426600-13443800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr18:13426800-13428000	Strong transcription	Fetal Thymus	thymus
42	chr18:13426800-13429600	Weak transcription	Primary T cells from cord blood	blood
43	chr18:13426800-13432400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr18:13426800-13433800	Weak transcription	Dnd41	blood
45	chr18:13426800-13435400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr18:13427000-13428000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr18:13427200-13428600	Enhancers	HUVEC	blood vessel
48	chr18:13427400-13429200	Enhancers	Brain Substantia Nigra	brain
49	chr18:13427400-13429200	Enhancers	Lung	lung
50	chr18:13427400-13441200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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