Variant report

Variant	rs3128386
Chromosome Location	chr7:112111863-112111864
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:112062614..112065098-chr7:112110254..112112226,2	MCF-7	breast:
2	chr7:112110317..112112313-chr7:112114863..112117342,2	MCF-7	breast:
3	chr7:112088943..112098465-chr7:112111106..112127214,31	K562	blood:
4	chr7:112111349..112114011-chr7:112120654..112122714,2	MCF-7	breast:
5	chr7:112098595..112101402-chr7:112109772..112113023,4	K562	blood:
6	chr7:112108188..112112481-chr7:112118688..112121294,3	MCF-7	breast:
7	chr7:112109911..112112772-chr7:112114561..112118551,4	K562	blood:
8	chr7:112105277..112107837-chr7:112109982..112112737,2	MCF-7	breast:
9	chr7:112110260..112112792-chr7:112132236..112134021,2	K562	blood:
10	chr7:112089590..112091914-chr7:112111290..112113718,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000006652	Chromatin interaction
ENSG00000181016	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1468457	0.94[AFR][1000 genomes]
rs1468458	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs2074796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2529588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708610	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2708611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3095025	1.00[ASN][1000 genomes]
rs3109112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3128388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3183621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34633971	0.91[AFR][1000 genomes]
rs3801795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3807213	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs4386904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6966318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6967593	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7467	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[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	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1030033	chr7:112092709-112140430	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3128386	LSMEM1	cis	Thyroid	GTEx
rs3128386	IFRD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112092600-112121800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:112094000-112118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:112094000-112121400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:112094400-112118200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:112094600-112114800	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr7:112094600-112117000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:112095000-112114200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:112095200-112117400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr7:112095400-112117200	Strong transcription	Dnd41	blood
10	chr7:112095600-112116400	Strong transcription	NH-A	brain
11	chr7:112095600-112116600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr7:112095600-112117200	Strong transcription	HSMM	muscle
13	chr7:112095600-112117400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:112095600-112117400	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr7:112095600-112117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr7:112095600-112118800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:112095800-112114600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:112095800-112117000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr7:112095800-112117000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr7:112095800-112117400	Strong transcription	Fetal Thymus	thymus
21	chr7:112095800-112118000	Strong transcription	Placenta	Placenta
22	chr7:112095800-112118200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:112095800-112118200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:112096000-112116800	Strong transcription	HUVEC	blood vessel
25	chr7:112096400-112121600	Strong transcription	Liver	Liver
26	chr7:112096400-112121800	Weak transcription	Stomach Mucosa	stomach
27	chr7:112096800-112117600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr7:112100600-112112800	Weak transcription	Pancreas	Pancrea
29	chr7:112100600-112135000	Weak transcription	Esophagus	oesophagus
30	chr7:112101000-112114400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:112101000-112118000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr7:112102400-112117400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr7:112102600-112117800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr7:112102800-112116600	Strong transcription	A549	lung
35	chr7:112102800-112119800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr7:112103000-112114600	Strong transcription	NHDF-Ad	bronchial
37	chr7:112103000-112116600	Strong transcription	HMEC	breast
38	chr7:112103000-112116800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:112103000-112117400	Strong transcription	Adipose Nuclei	Adipose
40	chr7:112103000-112117800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr7:112103000-112118200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:112103000-112118200	Strong transcription	Hela-S3	cervix
43	chr7:112103000-112119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr7:112103200-112117600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:112103200-112118200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:112103200-112118200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:112103200-112118600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:112103400-112117200	Strong transcription	Osteobl	bone
49	chr7:112103600-112115400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr7:112103600-112121200	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links