Variant report

Variant	rs3748107
Chromosome Location	chr7:66479228-66479229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10950058	0.83[ASN][1000 genomes]
rs12534892	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12540243	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12540298	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1879852	0.91[ASN][1000 genomes]
rs1879853	0.82[ASN][1000 genomes]
rs3864349	0.86[ASN][1000 genomes]
rs4610623	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55694864	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59248739	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59775098	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62466615	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62466617	0.81[EUR][1000 genomes]
rs62466619	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62466623	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62466626	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62466627	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7806639	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[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	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1032575	chr7:66432853-66576034	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv981515	chr7:66477535-66532313	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3748107	TYW1	cis	parietal	SCAN
rs3748107	VKORC1L1	cis	parietal	SCAN
rs3748107	ERV3	cis	cerebellum	SCAN
rs3748107	RABGEF1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66462200-66482600	Weak transcription	Aorta	Aorta
2	chr7:66462400-66479400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:66462400-66482200	Weak transcription	Small Intestine	intestine
4	chr7:66462400-66482600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr7:66462400-66490000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:66462400-66496000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:66462400-66500200	Weak transcription	Psoas Muscle	Psoas
8	chr7:66462400-66508000	Weak transcription	Stomach Mucosa	stomach
9	chr7:66462600-66480600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:66462600-66482800	Weak transcription	NHEK	skin
11	chr7:66462600-66484600	Weak transcription	HUVEC	blood vessel
12	chr7:66462600-66487600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:66462600-66497200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr7:66462800-66494600	Weak transcription	Esophagus	oesophagus
15	chr7:66463000-66487200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:66463000-66507800	Weak transcription	Fetal Brain Male	brain
17	chr7:66463200-66482600	Weak transcription	HMEC	breast
18	chr7:66463200-66483000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr7:66463200-66484800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:66463200-66487400	Weak transcription	NH-A	brain
21	chr7:66463200-66510000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr7:66467000-66480600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:66468600-66484400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:66469000-66480600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:66469000-66484400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:66469200-66479800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:66469200-66482800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr7:66470000-66489000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:66470000-66489000	Strong transcription	Fetal Intestine Small	intestine
30	chr7:66470200-66488200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr7:66470200-66488400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr7:66470200-66488400	Strong transcription	Fetal Stomach	stomach
33	chr7:66470200-66492200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr7:66470400-66484400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr7:66470400-66488000	Strong transcription	Dnd41	blood
36	chr7:66470400-66489000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr7:66470400-66495200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr7:66470600-66481000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:66470600-66485400	Strong transcription	Placenta	Placenta
40	chr7:66470600-66492600	Strong transcription	Liver	Liver
41	chr7:66470600-66494800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr7:66470800-66481200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:66470800-66481600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr7:66472200-66481000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:66472400-66481600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr7:66472400-66484600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:66472400-66485400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr7:66472600-66483400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr7:66472600-66487000	Weak transcription	A549	lung
50	chr7:66472800-66484400	Weak transcription	Hela-S3	cervix

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