Variant report

Variant	rs425013
Chromosome Location	chr7:107840971-107840972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107840057..107842255-chr7:107937956..107941774,3	MCF-7	breast:
2	chr7:107840521..107844716-chr7:107989632..107993969,4	MCF-7	breast:
3	chr7:107840154..107842979-chr7:107937702..107939902,2	MCF-7	breast:
4	chr7:107838620..107843312-chr7:108093150..108098167,6	MCF-7	breast:
5	chr7:107840763..107848322-chr7:108091812..108097680,8	MCF-7	breast:
6	chr7:107840675..107842857-chr7:107846031..107847571,2	K562	blood:
7	chr7:107839156..107844072-chr7:107845606..107848458,6	K562	blood:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12669568	0.82[CHD][hapmap]
rs12670313	0.80[CEU][hapmap]
rs1269627	0.90[ASN][1000 genomes]
rs17155301	0.82[CHD][hapmap]
rs2072320	0.82[ASN][1000 genomes]
rs2272618	0.82[CHD][hapmap]
rs2284280	0.85[CEU][hapmap]
rs369800	1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs369884	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs379986	0.88[ASN][1000 genomes]
rs381318	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs382932	0.95[ASN][1000 genomes]
rs383341	0.88[ASN][1000 genomes]
rs392704	0.81[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs392976	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs393245	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs397179	0.88[ASN][1000 genomes]
rs397704	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs402029	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs404287	0.94[ASW][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs404453	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs409724	0.80[CEU][hapmap]
rs409797	0.80[CEU][hapmap]
rs409969	0.80[CEU][hapmap]
rs449540	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs449711	0.88[ASN][1000 genomes]
rs4730291	0.80[CEU][hapmap]
rs61040788	0.88[ASN][1000 genomes]
rs6958498	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6964394	0.82[ASN][1000 genomes]
rs6978315	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7777322	0.82[CHD][hapmap]
rs7784353	0.81[CHD][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs425013	LAMB4	cis	cerebellum	SCAN

Chromatin state (count:38 , 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	chr7:107820800-107846800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:107820800-107850600	Weak transcription	Fetal Intestine Large	intestine
8	chr7:107820800-107851200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:107821000-107852200	Weak transcription	Fetal Muscle Leg	muscle
10	chr7:107821600-107850400	Weak transcription	Fetal Brain Male	brain
11	chr7:107828000-107852000	Weak transcription	Pancreas	Pancrea
12	chr7:107828800-107846600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:107828800-107851400	Weak transcription	Fetal Intestine Small	intestine
14	chr7:107829600-107848600	Weak transcription	Brain Anterior Caudate	brain
15	chr7:107830400-107857200	Weak transcription	Fetal Brain Female	brain
16	chr7:107830400-107886400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:107834800-107841800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:107835000-107851400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:107835400-107841600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr7:107835400-107845400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:107835600-107844200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:107836000-107844800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:107836600-107843200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr7:107836800-107851200	Weak transcription	HMEC	breast
25	chr7:107836800-107852000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:107838400-107841800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr7:107838600-107844400	Weak transcription	HUVEC	blood vessel
28	chr7:107839200-107841000	Strong transcription	A549	lung
29	chr7:107839400-107841200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:107839400-107843400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr7:107840000-107841000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:107840200-107841000	Enhancers	NHEK	skin
33	chr7:107840400-107841200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr7:107840600-107841000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr7:107840600-107841400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:107840800-107841000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:107840800-107841000	Enhancers	Placenta	Placenta
38	chr7:107840800-107841200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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