Variant report

Variant	rs1269657
Chromosome Location	chr7:107907326-107907327
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:107897446..107899734-chr7:107904725..107907661,2	K562	blood:
2	chr7:107905891..107908548-chr7:107908939..107910827,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12111776	1.00[CHB][hapmap]
rs12111953	1.00[CHB][hapmap]
rs1269630	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1269631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1269632	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1269633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1269637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1269638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1269644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1269646	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1269647	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1269654	1.00[CHB][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs1544677	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17134753	1.00[CHB][hapmap]
rs17155059	1.00[CHB][hapmap]
rs17155074	1.00[CHB][hapmap]
rs17155081	1.00[CHB][hapmap]
rs17155094	1.00[CHB][hapmap]
rs17155125	1.00[CHB][hapmap]
rs17333297	1.00[CHD][hapmap]
rs382751	1.00[CHB][hapmap]
rs394921	1.00[CHB][hapmap]
rs399849	1.00[CHB][hapmap]
rs401573	1.00[CHB][hapmap]
rs41409846	1.00[CHD][hapmap]
rs420889	1.00[CHB][hapmap]
rs449919	1.00[CHB][hapmap]
rs4727701	0.87[EUR][1000 genomes]
rs6466219	1.00[CHB][hapmap]
rs6974903	1.00[CHB][hapmap]

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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1269657	RINT1	cis	parietal	SCAN
rs1269657	COX5B	trans	cerebellum	SCAN
rs1269657	LAMB4	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107887400-107925000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:107893200-107907400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:107901600-107907800	Enhancers	Fetal Muscle Leg	muscle
4	chr7:107904000-107908600	Weak transcription	Brain Angular Gyrus	brain
5	chr7:107904000-107910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:107904400-107907400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr7:107904800-107909000	Weak transcription	HSMMtube	muscle
8	chr7:107906000-107911000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:107906600-107907400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:107906600-107908000	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr7:107906600-107909600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:107906800-107907400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:107906800-107907400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr7:107906800-107907600	Enhancers	Fetal Brain Female	brain
15	chr7:107906800-107907800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:107906800-107907800	Enhancers	NH-A	brain
17	chr7:107907000-107907400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:107907000-107907400	Enhancers	Brain Anterior Caudate	brain
19	chr7:107907000-107907400	Enhancers	Brain Hippocampus Middle	brain
20	chr7:107907000-107907400	Enhancers	HUVEC	blood vessel
21	chr7:107907000-107908800	Weak transcription	HSMM	muscle
22	chr7:107907000-107911400	Enhancers	A549	lung
23	chr7:107907200-107908400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:107907200-107923400	Weak transcription	Fetal Brain Male	brain

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