Variant report

Variant	rs1538140
Chromosome Location	chr1:224030498-224030499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224011037..224013548-chr1:224029939..224032384,3	MCF-7	breast:
2	chr1:223997873..223999794-chr1:224029438..224032178,2	MCF-7	breast:
3	chr1:224000966..224003720-chr1:224029904..224032182,2	MCF-7	breast:
4	chr1:224010151..224012081-chr1:224029415..224031184,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1003061	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1153928	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1153937	0.84[ASN][1000 genomes]
rs1153938	0.83[ASN][1000 genomes]
rs1153943	0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1153944	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1153946	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1153950	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1153952	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1153954	0.91[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1153956	0.83[AMR][1000 genomes]
rs1222081	1.00[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1222123	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1222126	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1222127	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1222147	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1222148	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1222153	0.89[CHB][hapmap];0.83[GIH][hapmap]
rs1222158	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1228475	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17739	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1982611	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60739082	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6604726	0.89[EUR][1000 genomes]
rs6658724	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6661816	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6667215	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6694471	0.95[EUR][1000 genomes]
rs6698919	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs898878	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1538140	HLX	cis	parietal	SCAN
rs1538140	DEGS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224020600-224032400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:224020800-224031600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:224023000-224030600	Weak transcription	Fetal Kidney	kidney
4	chr1:224023200-224031600	Weak transcription	Hela-S3	cervix
5	chr1:224024000-224031800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:224024000-224031800	Weak transcription	Thymus	Thymus
7	chr1:224024200-224031600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:224024200-224031600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:224024200-224031600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:224024200-224031800	Weak transcription	Adipose Nuclei	Adipose
11	chr1:224024400-224031800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:224024600-224030800	Weak transcription	Primary B cells from cord blood	blood
13	chr1:224024600-224031600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:224024600-224031800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:224024600-224031800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:224024600-224031800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:224024600-224031800	Weak transcription	Esophagus	oesophagus
18	chr1:224025200-224030600	Weak transcription	NHEK	skin
19	chr1:224025200-224031800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:224025600-224032200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:224026000-224031600	Weak transcription	Fetal Intestine Small	intestine
22	chr1:224026200-224031800	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:224026400-224030600	Weak transcription	HepG2	liver
24	chr1:224026400-224030600	Weak transcription	HUVEC	blood vessel
25	chr1:224026400-224031600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:224026400-224031600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:224026400-224031600	Weak transcription	Fetal Intestine Large	intestine
28	chr1:224026400-224031600	Weak transcription	Right Atrium	heart
29	chr1:224026400-224031600	Weak transcription	Stomach Mucosa	stomach
30	chr1:224026400-224031800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:224026400-224031800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:224026400-224031800	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:224026400-224031800	Weak transcription	Fetal Thymus	thymus
34	chr1:224026400-224031800	Weak transcription	Gastric	stomach
35	chr1:224026400-224031800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:224026400-224032400	Weak transcription	Lung	lung
37	chr1:224026400-224032600	Weak transcription	Spleen	Spleen
38	chr1:224026600-224030600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:224026600-224030600	Weak transcription	Brain Germinal Matrix	brain
40	chr1:224026600-224031600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:224026600-224031600	Weak transcription	Fetal Stomach	stomach
42	chr1:224026600-224031600	Weak transcription	Right Ventricle	heart
43	chr1:224026600-224031800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:224026800-224031600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:224026800-224031800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:224027000-224030600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:224027000-224031600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:224027200-224030600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:224027200-224031800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:224027800-224030600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links