Variant report

Variant	rs4150661
Chromosome Location	chr11:18379629-18379630
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18378755..18381562-chr11:18416163..18418318,3	K562	blood:
2	chr11:18377382..18380490-chr11:18416157..18418987,3	K562	blood:
3	chr11:18350549..18352457-chr11:18378892..18380710,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LDHA-1	chr11:18379499-18379649	NONHSAT018279

Variant related genes	Relation type
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10734259	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10741741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741742	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832917	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10832921	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024634	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1140047	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12286683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12293544	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1520884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2061164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2124374	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3740711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802968	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3825025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150526	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4150550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150566	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150588	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150609	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4150612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4150650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150653	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4757637	1.00[CHB][hapmap]
rs4757645	0.86[CEU][hapmap]
rs6486419	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7103375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7129995	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7947378	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9783347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9988866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4150661	LDHAL6A	cis	cerebellum	SCAN
rs4150661	NELL1	cis	parietal	SCAN
rs4150661	GTF2H1	cis	Esophagus Muscularis	GTEx
rs4150661	GTF2H1	cis	parietal	SCAN
rs4150661	GTF2H1	cis	Esophagus Mucosa	GTEx
rs4150661	HPS5	cis	parietal	SCAN
rs4150661	LDHA	cis	parietal	SCAN
rs4150661	HPS5	cis	cerebellum	SCAN
rs4150661	GTF2H1	cis	Stomach	GTEx
rs4150661	ABCC8	cis	parietal	SCAN
rs4150661	GTF2H1	cis	cerebellum	SCAN
rs4150661	PIK3C2A	cis	cerebellum	SCAN
rs4150661	GTF2H1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18345000-18383200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:18346800-18382800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:18346800-18390400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:18347000-18387400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:18351200-18387000	Weak transcription	Stomach Mucosa	stomach
7	chr11:18352400-18389000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:18354400-18389400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:18357000-18389200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:18360000-18382200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:18361800-18391600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:18363000-18390200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:18363200-18393000	Weak transcription	Fetal Heart	heart
14	chr11:18365800-18381400	Weak transcription	Pancreas	Pancrea
15	chr11:18366600-18381400	Weak transcription	Gastric	stomach
16	chr11:18367600-18390000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:18368000-18382400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:18368200-18379800	Weak transcription	Fetal Brain Male	brain
19	chr11:18368600-18381400	Weak transcription	Spleen	Spleen
20	chr11:18369600-18385800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:18369800-18380600	Weak transcription	NHLF	lung
22	chr11:18370200-18379800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:18370400-18380000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr11:18370600-18379800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:18372800-18387200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr11:18373200-18386000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:18373200-18388200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:18373200-18389200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr11:18373200-18389200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:18373200-18389200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:18373200-18390600	Strong transcription	Adipose Nuclei	Adipose
32	chr11:18373400-18381800	Strong transcription	Primary B cells from cord blood	blood
33	chr11:18373400-18385600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:18373400-18388200	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr11:18373400-18389200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr11:18373400-18390000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:18373400-18390400	Strong transcription	Dnd41	blood
38	chr11:18373600-18389200	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr11:18373600-18389800	Strong transcription	Liver	Liver
40	chr11:18373600-18389800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr11:18373600-18390200	Strong transcription	Fetal Thymus	thymus
42	chr11:18373600-18390400	Strong transcription	Placenta	Placenta
43	chr11:18373600-18391200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:18373800-18384000	Strong transcription	Primary T cells from cord blood	blood
45	chr11:18373800-18387200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:18373800-18387600	Strong transcription	Ovary	ovary
47	chr11:18373800-18388000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr11:18373800-18389200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr11:18373800-18389200	Strong transcription	Fetal Intestine Large	intestine
50	chr11:18373800-18389200	Strong transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links