Variant report

Variant	rs6691932
Chromosome Location	chr1:113144263-113144264
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113142744..113144824-chr1:113152085..113154439,2	K562	blood:
2	chr1:113142242..113147052-chr1:113160785..113163807,5	K562	blood:
3	chr1:113143618..113146588-chr1:113149750..113152817,3	K562	blood:
4	chr1:113143142..113146468-chr1:113154015..113156949,3	MCF-7	breast:
5	chr1:113138487..113142157-chr1:113142308..113146273,3	K562	blood:
6	chr1:113144240..113147645-chr1:113160783..113163246,3	MCF-7	breast:
7	chr1:113142791..113145357-chr1:113176372..113179139,2	K562	blood:
8	chr1:113139567..113142157-chr1:113143590..113146632,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000116489	Chromatin interaction
ENSG00000252750	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1001494	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1006298	0.82[EUR][1000 genomes]
rs10745330	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10776756	0.81[EUR][1000 genomes]
rs10857963	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11102497	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11102512	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12046329	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12046466	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12126277	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12728001	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1994604	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932532	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2932536	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2999154	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2999155	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2999157	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3013431	0.80[ASN][1000 genomes]
rs3013439	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3013440	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3103450	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs351372	0.82[EUR][1000 genomes]
rs6537743	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6666579	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6669096	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6682737	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700673	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7415820	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7513716	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7524494	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7544663	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7546094	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554345	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7554916	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs902289	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs910697	0.80[EUR][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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6691932	ST7L	cis	Stomach	GTEx
rs6691932	ST7L	cis	lung	GTEx
rs6691932	ST7L	cis	multi-tissue	Pritchard
rs6691932	ST7L	cis	Heart Left Ventricle	GTEx
rs6691932	ENSG00000007341	cis	multi-tissue	Pritchard
rs6691932	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs6691932	ST7L	cis	Thyroid	GTEx
rs6691932	ST7L	cis	Adipose Subcutaneous	GTEx
rs6691932	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs6691932	ST7L	cis	Esophagus Muscularis	GTEx
rs6691932	ST7L	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
2	chr1:113109000-113160000	Weak transcription	Gastric	stomach
3	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
5	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
6	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
7	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:113121000-113148400	Weak transcription	Stomach Mucosa	stomach
10	chr1:113124600-113148400	Weak transcription	NHLF	lung
11	chr1:113128000-113148400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:113129000-113147200	Strong transcription	HSMM	muscle
13	chr1:113129600-113159000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:113131400-113160000	Weak transcription	Fetal Heart	heart
15	chr1:113131600-113147200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:113132600-113148400	Weak transcription	Lung	lung
17	chr1:113132600-113148400	Weak transcription	Pancreas	Pancrea
18	chr1:113132600-113148400	Weak transcription	Thymus	Thymus
19	chr1:113132600-113152400	Weak transcription	Psoas Muscle	Psoas
20	chr1:113132600-113154800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:113132600-113159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:113132800-113145400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:113133000-113148400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:113133000-113148400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:113133000-113148600	Weak transcription	HSMMtube	muscle
26	chr1:113133000-113152000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:113133000-113152400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:113133000-113160000	Weak transcription	Fetal Brain Male	brain
29	chr1:113133000-113160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:113133200-113146800	Weak transcription	Fetal Thymus	thymus
31	chr1:113133200-113148400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:113133200-113148400	Weak transcription	GM12878-XiMat	blood
33	chr1:113133200-113148600	Weak transcription	A549	lung
34	chr1:113133200-113149800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:113133200-113150800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:113133200-113159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:113133200-113159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:113133600-113148400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:113135400-113159800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:113136000-113147400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:113136200-113147400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:113136200-113156800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:113136600-113158800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:113136800-113145400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr1:113136800-113159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:113137000-113154200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:113137600-113160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:113138000-113159400	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:113138400-113147400	Strong transcription	Liver	Liver
50	chr1:113138600-113146600	Strong transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links