Variant report

Variant	rs1269632
Chromosome Location	chr7:107874906-107874907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107874226..107876380-chr7:107878997..107880682,2	MCF-7	breast:
2	chr7:107864802..107867647-chr7:107872960..107875174,3	MCF-7	breast:
3	chr7:107874811..107876975-chr7:107889006..107891244,2	K562	blood:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1269631	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269633	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269637	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269638	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269644	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1269646	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269647	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269654	1.00[CHB][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs1269657	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]
rs1544677	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[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];0.90[ASN][1000 genomes]
rs41409846	1.00[CHD][hapmap]
rs420889	1.00[CHB][hapmap]
rs449919	1.00[CHB][hapmap]
rs4727701	0.91[EUR][1000 genomes];1.00[ASN][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	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv831089	chr7:107687618-107877240	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1269632	RINT1	cis	parietal	SCAN
rs1269632	LAMB4	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107830400-107886400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr7:107852200-107875600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:107852400-107875600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:107852400-107876000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:107860600-107886600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:107863200-107876000	Weak transcription	Pancreas	Pancrea
7	chr7:107863600-107876200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:107863800-107876000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:107863800-107876200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr7:107863800-107877200	Weak transcription	Fetal Muscle Leg	muscle
11	chr7:107867800-107878000	Weak transcription	Brain Angular Gyrus	brain
12	chr7:107870000-107876000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr7:107870600-107876600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:107871200-107875800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:107871200-107876000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:107871200-107880000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:107871200-107886400	Weak transcription	Brain Anterior Caudate	brain
18	chr7:107871600-107879800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:107873600-107875000	Enhancers	Fetal Intestine Large	intestine
20	chr7:107873800-107875000	Enhancers	Small Intestine	intestine
21	chr7:107873800-107877000	Enhancers	HSMM	muscle
22	chr7:107874200-107875200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:107874200-107876600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:107874200-107876600	Enhancers	Osteobl	bone
25	chr7:107874200-107876800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:107874400-107875000	Enhancers	HUVEC	blood vessel
27	chr7:107874400-107875600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr7:107874400-107875800	Enhancers	K562	blood
29	chr7:107874400-107876600	Enhancers	NHDF-Ad	bronchial
30	chr7:107874400-107879200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr7:107874600-107875200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr7:107874600-107875200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr7:107874600-107875200	Enhancers	Fetal Intestine Small	intestine
34	chr7:107874600-107876400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:107874600-107876400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:107874600-107876400	Flanking Active TSS	A549	lung
37	chr7:107874600-107876400	Enhancers	NHEK	skin
38	chr7:107874600-107876600	Enhancers	NHLF	lung
39	chr7:107874600-107876800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr7:107874600-107877000	Enhancers	HMEC	breast
41	chr7:107874600-107878000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:107874800-107875000	Enhancers	Placenta	Placenta
43	chr7:107874800-107875400	Weak transcription	Adipose Nuclei	Adipose
44	chr7:107874800-107876400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:107874800-107876600	Enhancers	HepG2	liver
46	chr7:107874800-107876600	Enhancers	NH-A	brain
47	chr7:107874800-107886200	Weak transcription	HSMMtube	muscle

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