Variant report

Variant	rs402142
Chromosome Location	chr7:107830774-107830775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107826342..107829124-chr7:107830145..107834558,4	K562	blood:
2	chr7:107829350..107831359-chr7:107833411..107835612,3	K562	blood:
3	chr7:107819867..107822378-chr7:107829973..107832574,2	K562	blood:
4	chr7:107829005..107831347-chr7:107833013..107835060,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10233338	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs107588	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs107589	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2079710	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2142325	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs371215	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs371613	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819740	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3819742	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3819743	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3819744	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3819745	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs385432	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs393266	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs398268	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs399543	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs401433	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs401573	0.89[EUR][1000 genomes]
rs414892	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs417455	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs422327	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423193	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426551	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs427909	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs433870	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs438272	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs439155	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439652	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs439657	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs441534	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730294	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4730295	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4730296	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6943271	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6959831	0.83[AMR][1000 genomes]
rs6962066	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6970656	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv888941	chr7:107796150-107863395	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1030222	chr7:107809927-107844916	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107786800-107857800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:107787800-107844200	Weak transcription	Brain Germinal Matrix	brain
3	chr7:107818200-107851800	Weak transcription	HSMMtube	muscle
4	chr7:107818600-107848400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:107820600-107867400	Weak transcription	Brain Angular Gyrus	brain
6	chr7:107820800-107834600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:107820800-107840800	Weak transcription	Placenta	Placenta
8	chr7:107820800-107846800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:107820800-107850600	Weak transcription	Fetal Intestine Large	intestine
10	chr7:107820800-107851200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:107821000-107852200	Weak transcription	Fetal Muscle Leg	muscle
12	chr7:107821600-107850400	Weak transcription	Fetal Brain Male	brain
13	chr7:107822000-107834000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr7:107822400-107832200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:107823200-107834400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:107823400-107833800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:107826800-107833800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr7:107827600-107836600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:107827800-107836000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr7:107828000-107852000	Weak transcription	Pancreas	Pancrea
21	chr7:107828400-107832000	Enhancers	NHEK	skin
22	chr7:107828600-107838200	Strong transcription	A549	lung
23	chr7:107828800-107831600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:107828800-107846600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:107828800-107851400	Weak transcription	Fetal Intestine Small	intestine
26	chr7:107829400-107830800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:107829600-107831000	Enhancers	GM12878-XiMat	blood
28	chr7:107829600-107848600	Weak transcription	Brain Anterior Caudate	brain
29	chr7:107830000-107830800	Enhancers	Primary T cells from cord blood	blood
30	chr7:107830000-107830800	Enhancers	Fetal Thymus	thymus
31	chr7:107830000-107831000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr7:107830200-107834400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:107830200-107836200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:107830400-107830800	Weak transcription	Thymus	Thymus
35	chr7:107830400-107831000	Weak transcription	HSMM	muscle
36	chr7:107830400-107831600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:107830400-107832200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:107830400-107839800	Weak transcription	Brain Substantia Nigra	brain
39	chr7:107830400-107857200	Weak transcription	Fetal Brain Female	brain
40	chr7:107830400-107886400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr7:107830600-107831800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:107830600-107833800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:107830600-107834200	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links