Variant report

Variant	rs1891707
Chromosome Location	chr1:112931238-112931239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:112930750..112936540-chr1:113240694..113246273,6	MCF-7	breast:
2	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
3	chr1:112920907..112923373-chr1:112930498..112932173,2	K562	blood:
4	chr1:112930286..112934243-chr1:113005745..113008841,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155363	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs12080074	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138024	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1419041	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1891705	0.87[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2488762	0.88[CHD][hapmap];1.00[MEX][hapmap]
rs2488765	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2488766	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2488768	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2488769	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2488770	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2492501	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2492502	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2492503	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2492504	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2999472	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4240532	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66475864	0.86[ASN][1000 genomes]
rs7415832	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1891707	CTTNBP2NL	cis	parietal	SCAN
rs1891707	CTTNBP2NL	Cis_1M	lymphoblastoid	RTeQTL
rs1891707	CTTNBP2NL	cis	lymphoblastoid	seeQTL
rs1891707	C1orf59	cis	parietal	SCAN
rs1891707	HBXIP	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112926800-112933200	Weak transcription	Pancreas	Pancrea
2	chr1:112926800-112933800	Weak transcription	Gastric	stomach
3	chr1:112927200-112933800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:112928600-112932600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:112928600-112933400	Enhancers	Fetal Intestine Large	intestine
6	chr1:112929200-112933200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:112929400-112933600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:112929600-112932200	Enhancers	HepG2	liver
9	chr1:112929600-112933400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:112930800-112931400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr1:112930800-112931600	Enhancers	Adipose Nuclei	Adipose
12	chr1:112930800-112931800	Flanking Active TSS	HUVEC	blood vessel
13	chr1:112931000-112931400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:112931000-112931400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:112931000-112931600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr1:112931000-112931600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:112931000-112931600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:112931000-112931600	Enhancers	HMEC	breast
19	chr1:112931000-112931600	Enhancers	NHDF-Ad	bronchial
20	chr1:112931000-112931800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:112931000-112931800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:112931000-112932000	Enhancers	NH-A	brain
23	chr1:112931000-112932400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:112931000-112932600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:112931000-112933200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:112931000-112933200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr1:112931000-112933200	Enhancers	Osteobl	bone
28	chr1:112931200-112931400	Enhancers	Esophagus	oesophagus
29	chr1:112931200-112931400	Bivalent Enhancer	Pancreatic Islets	Pancreatic Islet
30	chr1:112931200-112931600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr1:112931200-112931600	Enhancers	H1 Cell Line	embryonic stem cell
32	chr1:112931200-112931600	Enhancers	H9 Cell Line	embryonic stem cell
33	chr1:112931200-112931600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr1:112931200-112931600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:112931200-112931600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:112931200-112931600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:112931200-112931600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:112931200-112931600	Enhancers	Placenta	Placenta
39	chr1:112931200-112932200	Weak transcription	Brain Anterior Caudate	brain
40	chr1:112931200-112932200	Enhancers	HSMM	muscle
41	chr1:112931200-112932600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:112931200-112933000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr1:112931200-112933600	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links