Variant report

Variant	rs40245
Chromosome Location	chr7:21470536-21470537
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:21448504..21451103-chr7:21469416..21470988,2	K562	blood:
2	chr7:21449603..21452420-chr7:21469416..21471792,2	K562	blood:
3	chr7:21465891..21468738-chr7:21469069..21472897,3	MCF-7	breast:
4	chr7:21470159..21472152-chr7:21472473..21475281,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105866	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1013716	0.83[CEU][hapmap]
rs10269168	0.88[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10272006	0.83[CEU][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs11971316	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11983472	0.82[JPT][hapmap]
rs12534852	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12537609	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12668354	0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12672629	0.85[JPT][hapmap];0.86[AFR][1000 genomes]
rs12673975	0.81[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2158414	0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2237303	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs2282888	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2390539	0.85[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28541530	0.89[AFR][1000 genomes]
rs3735440	0.83[CEU][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs41495348	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4397283	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4722031	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4722033	0.81[EUR][1000 genomes]
rs6461561	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6461562	0.82[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs6461568	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6948810	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6974974	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6978922	0.83[ASN][1000 genomes]
rs7780553	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7781732	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7792280	0.86[EUR][1000 genomes]
rs7798894	0.85[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7810841	0.83[CEU][hapmap]
rs9639377	0.90[CEU][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9639378	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[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	nsv1027302	chr7:21391598-21727016	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv538800	chr7:21391598-21727016	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1028434	chr7:21468437-21636671	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21468400-21490600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:21468400-21497800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:21468600-21470600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:21468600-21472200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr7:21468600-21476600	Weak transcription	NHEK	skin
6	chr7:21468600-21478800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:21468600-21488600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr7:21468600-21495600	Weak transcription	Fetal Intestine Large	intestine
9	chr7:21468800-21470600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
10	chr7:21468800-21470600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr7:21468800-21470800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:21468800-21471400	Weak transcription	Osteobl	bone
13	chr7:21468800-21471600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:21468800-21489000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:21468800-21493600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:21469000-21470600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:21469000-21470600	Flanking Active TSS	Fetal Brain Female	brain
18	chr7:21469000-21472000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
19	chr7:21469000-21472200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr7:21469000-21474800	Weak transcription	A549	lung
21	chr7:21469000-21483800	Weak transcription	Adipose Nuclei	Adipose
22	chr7:21469200-21470600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:21469200-21470600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
24	chr7:21469200-21470600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:21469200-21470800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr7:21469400-21470600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr7:21469400-21470600	Genic enhancers	Fetal Muscle Leg	muscle
28	chr7:21469400-21470600	Genic enhancers	Left Ventricle	heart
29	chr7:21469400-21470600	Enhancers	Right Atrium	heart
30	chr7:21469800-21470600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr7:21469800-21470600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
32	chr7:21469800-21470600	Enhancers	Right Ventricle	heart
33	chr7:21469800-21470800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
34	chr7:21469800-21471600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr7:21469800-21472000	Flanking Active TSS	Dnd41	blood
36	chr7:21469800-21472000	Weak transcription	NHLF	lung
37	chr7:21469800-21474400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:21470000-21470600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
39	chr7:21470000-21470600	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr7:21470000-21470800	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr7:21470000-21472400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr7:21470000-21488600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr7:21470000-21490400	Weak transcription	Fetal Kidney	kidney
44	chr7:21470000-21497800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr7:21470200-21470600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr7:21470200-21470600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr7:21470200-21470600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr7:21470200-21470600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr7:21470200-21470600	Active TSS	Brain Hippocampus Middle	brain
50	chr7:21470200-21470600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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