Variant report

Variant	rs11158538
Chromosome Location	chr14:64859191-64859192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:64852898..64856787-chr14:64858975..64865298,10	K562	blood:
2	chr14:64853586..64859592-chr14:64968792..64973445,7	MCF-7	breast:
3	chr14:64857964..64859917-chr14:64874810..64877403,2	MCF-7	breast:
4	chr14:64852868..64856787-chr14:64858237..64862286,8	K562	blood:
5	chr14:64857748..64860531-chr14:64970254..64972239,2	K562	blood:
6	chr14:64802845..64807201-chr14:64857442..64860661,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214770	Chromatin interaction
ENSG00000089775	Chromatin interaction
ENSG00000140009	Chromatin interaction
ENSG00000126804	Chromatin interaction
ENSG00000100714	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10131195	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10145700	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10146204	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1076991	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs11158537	0.96[ASN][1000 genomes]
rs11158539	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12100642	0.94[EUR][1000 genomes]
rs12434608	0.82[EUR][1000 genomes]
rs1256093	0.82[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1256095	0.80[TSI][hapmap]
rs12894546	0.82[EUR][1000 genomes]
rs28570137	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2983733	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2983736	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2983738	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2983739	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2983741	0.96[EUR][1000 genomes]
rs2983742	0.98[EUR][1000 genomes]
rs2983746	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2983747	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2987958	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2987959	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2987960	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2987961	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2987962	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2987963	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2987964	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2987965	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2987969	0.89[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2987970	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2987971	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2987972	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2987973	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2987974	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2987977	0.86[EUR][1000 genomes]
rs2987979	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2987982	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2987984	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3020436	0.92[ASW][hapmap];0.89[CEU][hapmap];0.96[GIH][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.94[EUR][1000 genomes]
rs3020438	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3020439	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3020441	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3020442	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35020344	0.82[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs36016358	0.82[EUR][1000 genomes]
rs3783731	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4902274	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56029832	0.99[ASN][1000 genomes]
rs57087457	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57351847	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57845486	0.96[ASN][1000 genomes]
rs7151163	1.00[CEU][hapmap];0.80[YRI][hapmap];0.99[EUR][1000 genomes]
rs72722376	0.96[ASN][1000 genomes]
rs8003153	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8006686	0.91[ASN][1000 genomes]
rs8007217	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8010584	0.96[EUR][1000 genomes]
rs8011839	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8015898	0.86[ASN][1000 genomes]
rs8018032	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8020827	0.85[ASN][1000 genomes]
rs9323449	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11158538	KCNH5	cis	parietal	SCAN
rs11158538	MTHFD1	cis	Thyroid	GTEx
rs11158538	MTHFD1	cis	parietal	SCAN
rs11158538	MTHFD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11158538	MTHFD1	cis	Artery Tibial	GTEx
rs11158538	MTHFD1	cis	cerebellum	SCAN
rs11158538	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64856000-64869800	Weak transcription	Placenta	Placenta
2	chr14:64856000-64886200	Weak transcription	Fetal Brain Male	brain
3	chr14:64856000-64913000	Weak transcription	Small Intestine	intestine
4	chr14:64856200-64860200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:64856200-64860200	Weak transcription	Ovary	ovary
6	chr14:64856200-64860200	Weak transcription	Right Ventricle	heart
7	chr14:64856200-64860400	Weak transcription	Spleen	Spleen
8	chr14:64856200-64861200	Weak transcription	Brain Substantia Nigra	brain
9	chr14:64856200-64867200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr14:64856200-64870400	Weak transcription	Fetal Brain Female	brain
11	chr14:64856200-64870400	Weak transcription	Fetal Intestine Large	intestine
12	chr14:64856200-64882200	Weak transcription	HSMMtube	muscle
13	chr14:64856200-64883800	Weak transcription	Esophagus	oesophagus
14	chr14:64856200-64885600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:64856200-64886400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr14:64856200-64931200	Weak transcription	Stomach Mucosa	stomach
17	chr14:64856400-64860200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr14:64856400-64860200	Weak transcription	Gastric	stomach
19	chr14:64856400-64861400	Weak transcription	Colonic Mucosa	Colon
20	chr14:64856400-64870400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr14:64856400-64870600	Weak transcription	Psoas Muscle	Psoas
22	chr14:64856400-64875800	Weak transcription	Thymus	Thymus
23	chr14:64856400-64877800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr14:64856400-64882400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr14:64856600-64859800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr14:64856600-64860200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr14:64856600-64861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr14:64856600-64867600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr14:64856600-64870600	Weak transcription	NH-A	brain
30	chr14:64856600-64879400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr14:64856800-64860200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr14:64856800-64860200	Weak transcription	Fetal Heart	heart
33	chr14:64856800-64862800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:64856800-64867200	Weak transcription	Brain Germinal Matrix	brain
35	chr14:64856800-64867400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:64856800-64868400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr14:64856800-64868400	Weak transcription	Osteobl	bone
38	chr14:64856800-64868600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr14:64856800-64868600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr14:64856800-64870400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr14:64856800-64870600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr14:64856800-64877800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr14:64856800-64881800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr14:64856800-64881800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr14:64856800-64882000	Weak transcription	Fetal Lung	lung
46	chr14:64856800-64882000	Weak transcription	NHLF	lung
47	chr14:64856800-64885800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr14:64857000-64860200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr14:64857000-64860400	Weak transcription	Primary T cells from cord blood	blood
50	chr14:64857000-64862800	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links