Variant report

Variant	rs392438
Chromosome Location	chr7:101688832-101688833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:60639525..60641886-chr7:101687189..101690169,2	MCF-7	breast:
2	chr7:101688104..101690930-chr7:101693641..101697108,3	MCF-7	breast:
3	chr20:60641089..60641822-chr7:101688169..101689168,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265306	Chromatin interaction
ENSG00000130699	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs382270	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs388781	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs391234	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs401301	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs401966	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs411656	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs421168	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs424478	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs425934	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs436483	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs450854	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7796231	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv482521	chr7:101604002-101718950	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv831080	chr7:101629121-101718950	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1027574	chr7:101654060-101718950	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv607985	chr7:101683563-101718950	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101642800-101697600	Weak transcription	Primary B cells from cord blood	blood
2	chr7:101656000-101689200	Weak transcription	Aorta	Aorta
3	chr7:101668000-101707200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:101668600-101694200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:101672200-101692200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:101672200-101697000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr7:101672400-101694000	Weak transcription	Primary T cells from cord blood	blood
8	chr7:101672400-101697200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:101673000-101689200	Weak transcription	Spleen	Spleen
10	chr7:101673200-101689200	Weak transcription	Pancreas	Pancrea
11	chr7:101673200-101692800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr7:101673200-101694200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:101674200-101707400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:101674400-101696800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:101674400-101697000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:101674800-101692600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr7:101679000-101695200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:101683400-101691400	Enhancers	GM12878-XiMat	blood
19	chr7:101683600-101689600	Weak transcription	Placenta	Placenta
20	chr7:101684000-101692200	Weak transcription	Fetal Intestine Large	intestine
21	chr7:101684200-101697400	Weak transcription	Liver	Liver
22	chr7:101685600-101697200	Weak transcription	HepG2	liver
23	chr7:101685800-101694000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:101685800-101694000	Weak transcription	NHEK	skin
25	chr7:101686000-101691000	Weak transcription	A549	lung
26	chr7:101686400-101694000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:101686800-101693800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr7:101687800-101689800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr7:101687800-101690000	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr7:101687800-101690400	Enhancers	Fetal Stomach	stomach
31	chr7:101687800-101690600	Enhancers	Fetal Heart	heart
32	chr7:101688000-101689000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:101688000-101689200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr7:101688000-101689200	Enhancers	Gastric	stomach
35	chr7:101688000-101689200	Flanking Active TSS	Osteobl	bone
36	chr7:101688000-101689400	Enhancers	Primary hematopoietic stem cells	blood
37	chr7:101688000-101689400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr7:101688000-101689400	Enhancers	Right Atrium	heart
39	chr7:101688000-101689400	Enhancers	Thymus	Thymus
40	chr7:101688000-101689600	Enhancers	Primary B cells from peripheral blood	blood
41	chr7:101688000-101689600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr7:101688000-101689600	Enhancers	Fetal Muscle Trunk	muscle
43	chr7:101688000-101689600	Enhancers	Fetal Thymus	thymus
44	chr7:101688000-101689800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:101688000-101690200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr7:101688000-101690200	Enhancers	Left Ventricle	heart
47	chr7:101688000-101690200	Enhancers	HSMM	muscle
48	chr7:101688000-101690800	Enhancers	Right Ventricle	heart
49	chr7:101688200-101689000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr7:101688200-101689200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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