Variant report

Variant	rs7554345
Chromosome Location	chr1:113122956-113122957
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113120348..113122221-chr1:113122499..113124584,2	K562	blood:
2	chr1:113120564..113122444-chr1:113122780..113125014,2	MCF-7	breast:
3	chr1:113122500..113125301-chr1:113129408..113131758,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1001494	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1006298	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10745330	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10776756	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10776757	0.81[EUR][1000 genomes]
rs10857963	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11102497	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11102512	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12046329	0.85[AMR][1000 genomes]
rs12046466	0.86[AMR][1000 genomes]
rs12126277	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12728001	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1994604	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932532	0.84[AMR][1000 genomes]
rs2932536	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2999154	0.87[AMR][1000 genomes]
rs2999155	0.87[AMR][1000 genomes]
rs2999157	0.83[AMR][1000 genomes]
rs3013439	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3013440	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3103450	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs351372	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4839254	0.80[EUR][1000 genomes]
rs6537743	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6666579	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6669096	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679414	0.82[EUR][1000 genomes]
rs6682737	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6691932	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6700673	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7415820	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7513716	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7524494	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544663	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7546094	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7554916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs902289	0.84[AMR][1000 genomes]
rs910697	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7554345	ST7L	cis	lung	GTEx
rs7554345	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs7554345	ST7L	cis	Adipose Subcutaneous	GTEx
rs7554345	ST7L	cis	Artery Tibial	GTEx
rs7554345	ST7L	cis	Stomach	GTEx
rs7554345	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs7554345	ST7L	cis	Esophagus Muscularis	GTEx
rs7554345	ST7L	cis	multi-tissue	Pritchard
rs7554345	ST7L	cis	Heart Left Ventricle	GTEx
rs7554345	ST7L	cis	Nerve Tibial	GTEx
rs7554345	ST7L	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
2	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
5	chr1:113081200-113132200	Weak transcription	Primary B cells from cord blood	blood
6	chr1:113081400-113132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:113081800-113132200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:113083200-113123200	Weak transcription	Right Atrium	heart
9	chr1:113084000-113131400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:113084800-113137000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:113087600-113125800	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:113088400-113132200	Weak transcription	HMEC	breast
13	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
14	chr1:113105400-113129800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:113109000-113123000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:113109000-113160000	Weak transcription	Gastric	stomach
17	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:113111000-113131000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:113111800-113138800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:113112000-113128200	Strong transcription	Liver	Liver
21	chr1:113112600-113131800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:113113200-113124400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:113113200-113132400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:113113800-113124400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:113114400-113124600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:113115000-113128800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:113115200-113123800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:113115200-113130200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:113115400-113123800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
31	chr1:113115800-113130800	Weak transcription	Fetal Brain Male	brain
32	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
33	chr1:113116000-113132400	Weak transcription	Thymus	Thymus
34	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
35	chr1:113116800-113124800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:113117000-113132200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:113117200-113125600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:113117200-113132200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:113117200-113132400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:113117400-113124000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:113117400-113125000	Strong transcription	Adipose Nuclei	Adipose
42	chr1:113117400-113132200	Weak transcription	GM12878-XiMat	blood
43	chr1:113117800-113124600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:113118400-113132400	Weak transcription	Brain Substantia Nigra	brain
46	chr1:113118600-113123800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:113118600-113132200	Weak transcription	A549	lung
48	chr1:113118800-113124800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:113118800-113126800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:113118800-113131200	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links