Variant report

Variant	rs1857966
Chromosome Location	chr1:209561715-209561716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209555303..209558478-chr1:209558595..209562675,4	MCF-7	breast:
2	chr1:209561204..209563175-chr1:209596060..209597812,2	MCF-7	breast:
3	chr1:209554903..209565803-chr1:209600283..209609508,22	MCF-7	breast:
4	chr1:209560392..209562273-chr1:209582844..209585455,2	MCF-7	breast:
5	chr1:209561394..209563113-chr1:209564950..209566663,2	MCF-7	breast:
6	chr1:209556562..209561769-chr1:209603992..209608152,7	MCF-7	breast:
7	chr1:209537992..209540217-chr1:209560334..209562277,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1014817	0.83[EUR][1000 genomes]
rs10494922	0.83[EUR][1000 genomes]
rs10494924	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17014326	0.80[EUR][1000 genomes]
rs2055698	0.91[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2356722	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2660642	0.80[CHB][hapmap]
rs6661759	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs906347	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs906348	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs906350	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs906351	0.90[CHB][hapmap];0.84[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209553200-209568600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:209555600-209564400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:209555800-209565200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:209557800-209565200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:209558000-209562000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:209558000-209566200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:209558200-209564400	Enhancers	HMEC	breast
8	chr1:209558400-209564400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:209559400-209565200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:209559400-209566000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:209560000-209563000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:209560400-209563600	Enhancers	HSMM	muscle
13	chr1:209560600-209562400	Enhancers	Hela-S3	cervix
14	chr1:209560600-209562600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:209560600-209563600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:209560800-209562400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:209560800-209563000	Enhancers	HSMMtube	muscle
18	chr1:209560800-209563200	Enhancers	Esophagus	oesophagus
19	chr1:209560800-209563400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:209560800-209563400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:209560800-209563400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:209560800-209563400	Enhancers	Osteobl	bone
23	chr1:209560800-209563600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:209560800-209563600	Enhancers	NH-A	brain
25	chr1:209560800-209563600	Enhancers	NHLF	lung
26	chr1:209560800-209565000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:209560800-209565600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:209561000-209563400	Enhancers	A549	lung
29	chr1:209561000-209565000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:209561000-209565400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:209561000-209571400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:209561200-209564200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:209561200-209567400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:209561400-209563200	Enhancers	NHDF-Ad	bronchial
35	chr1:209561600-209561800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:209561600-209562400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:209561600-209562600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:209561600-209563000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:209561600-209564400	Enhancers	NHEK	skin

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