Variant report

Variant	rs6669096
Chromosome Location	chr1:113132361-113132362
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113131312..113132892-chr1:113136156..113138926,2	K562	blood:
2	chr1:113132347..113134922-chr1:113161214..113163923,3	MCF-7	breast:
3	chr1:113130536..113134604-chr1:113155962..113159992,5	K562	blood:

Variant related genes	Relation type
ENSG00000116489	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs1001494	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1006298	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10745330	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10776756	0.86[EUR][1000 genomes]
rs10776757	0.80[EUR][1000 genomes]
rs10857963	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11102497	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11102512	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046329	0.83[AMR][1000 genomes]
rs12046466	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12126277	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12728001	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1994604	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932532	0.82[AMR][1000 genomes]
rs2932536	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2999154	0.85[AMR][1000 genomes]
rs2999155	0.85[AMR][1000 genomes]
rs2999157	0.81[AMR][1000 genomes]
rs3013439	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3013440	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3103450	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs351372	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4839254	0.81[EUR][1000 genomes]
rs6537743	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6666579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679414	0.82[EUR][1000 genomes]
rs6682737	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691932	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700673	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7415820	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7513716	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7524494	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544663	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7546094	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7554345	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7554916	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902289	0.82[AMR][1000 genomes]
rs910697	0.84[EUR][1000 genomes];0.84[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	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
rs6669096	ST7L	cis	Artery Tibial	GTEx
rs6669096	ST7L	cis	Adipose Subcutaneous	GTEx
rs6669096	ST7L	cis	multi-tissue	Pritchard
rs6669096	ST7L	cis	lung	GTEx
rs6669096	ST7L	cis	Thyroid	GTEx
rs6669096	ST7L	cis	Nerve Tibial	GTEx
rs6669096	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs6669096	ST7L	cis	Heart Left Ventricle	GTEx
rs6669096	ST7L	cis	Esophagus Muscularis	GTEx
rs6669096	ST7L	cis	Stomach	GTEx
rs6669096	ST7L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
2	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
3	chr1:113081400-113132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:113084800-113137000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
6	chr1:113109000-113160000	Weak transcription	Gastric	stomach
7	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:113111800-113138800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:113113200-113132400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
11	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
12	chr1:113116000-113132400	Weak transcription	Thymus	Thymus
13	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
14	chr1:113117200-113132400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:113118400-113132400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:113119000-113132400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:113119000-113138400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:113119200-113132400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:113119200-113132400	Weak transcription	Fetal Thymus	thymus
22	chr1:113121000-113132400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:113121000-113132600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:113121000-113148400	Weak transcription	Stomach Mucosa	stomach
25	chr1:113121200-113132400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:113121200-113132400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:113121800-113132800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr1:113122600-113133200	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:113123000-113132400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:113124600-113132400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr1:113124600-113148400	Weak transcription	NHLF	lung
32	chr1:113124800-113132400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:113125000-113142000	Weak transcription	Hela-S3	cervix
34	chr1:113126800-113132400	Weak transcription	K562	blood
35	chr1:113126800-113143400	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:113128000-113148400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:113129000-113147200	Strong transcription	HSMM	muscle
38	chr1:113129600-113159000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:113130000-113132400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:113130200-113133400	Strong transcription	NHDF-Ad	bronchial
41	chr1:113130200-113134200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:113130200-113141000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:113130400-113133000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:113130400-113133400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:113130600-113133400	Strong transcription	Adipose Nuclei	Adipose
46	chr1:113130800-113132400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:113130800-113132400	Strong transcription	Liver	Liver
48	chr1:113130800-113132400	Strong transcription	NH-A	brain
49	chr1:113130800-113132600	Strong transcription	NHEK	skin
50	chr1:113130800-113132800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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