Variant report

Variant	rs17055938
Chromosome Location	chr6:128831875-128831876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:197765766..197767854-chr6:128830235..128832178,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12526667	0.81[CEU][hapmap]
rs13437323	0.84[CEU][hapmap]
rs1417895	1.00[CHB][hapmap]
rs1417896	1.00[CHB][hapmap]
rs17364020	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17364090	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17364118	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17364153	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17461370	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1935131	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60719752	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425738	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62425739	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62425743	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62426790	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6569535	1.00[CHB][hapmap]
rs6569536	1.00[CHB][hapmap]
rs6920943	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6923822	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6935611	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7356823	1.00[CHB][hapmap]
rs73772047	0.87[ASN][1000 genomes]
rs7751265	1.00[CHB][hapmap]
rs7765212	0.82[CEU][hapmap]
rs9321121	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9375570	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9375572	1.00[CHB][hapmap]
rs9385464	1.00[CHB][hapmap]
rs9388638	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9388645	1.00[CHB][hapmap]
rs9388646	1.00[CHB][hapmap]
rs9402057	1.00[CHB][hapmap]
rs947358	1.00[ASN][1000 genomes]
rs9482892	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9491999	1.00[CHB][hapmap]
rs9492001	0.81[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128815200-128833800	Enhancers	Fetal Intestine Large	intestine
2	chr6:128817200-128839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:128817200-128839800	Weak transcription	Aorta	Aorta
4	chr6:128820600-128833800	Enhancers	Fetal Intestine Small	intestine
5	chr6:128821600-128836800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:128823400-128832800	Enhancers	Stomach Mucosa	stomach
7	chr6:128825800-128832400	Weak transcription	Fetal Kidney	kidney
8	chr6:128825800-128840000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:128828600-128832400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:128828600-128832800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:128828600-128833800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:128828600-128834000	Enhancers	NH-A	brain
13	chr6:128829000-128832400	Weak transcription	Gastric	stomach
14	chr6:128829000-128832400	Weak transcription	Right Atrium	heart
15	chr6:128829000-128834800	Weak transcription	Fetal Stomach	stomach
16	chr6:128829000-128836400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:128829200-128832200	Weak transcription	Fetal Lung	lung
18	chr6:128829400-128832400	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:128829400-128833800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:128829400-128836800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:128829400-128836800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:128829400-128837000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:128829400-128837400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:128829400-128839400	Weak transcription	Colonic Mucosa	Colon
25	chr6:128829400-128839600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:128829600-128832800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:128829600-128834000	Enhancers	NHDF-Ad	bronchial
28	chr6:128829800-128837400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:128830000-128832400	Weak transcription	Ovary	ovary
30	chr6:128830000-128832400	Weak transcription	Small Intestine	intestine
31	chr6:128830000-128834000	Enhancers	HMEC	breast
32	chr6:128830000-128839600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:128830400-128833000	Enhancers	Brain Substantia Nigra	brain
34	chr6:128830400-128833800	Enhancers	Brain Angular Gyrus	brain
35	chr6:128830400-128836800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:128830400-128837400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:128830600-128833800	Enhancers	Hela-S3	cervix
38	chr6:128830600-128834200	Enhancers	HepG2	liver
39	chr6:128831000-128832200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:128831000-128832600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:128831000-128834200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:128831200-128832200	Enhancers	A549	lung
43	chr6:128831200-128832200	Enhancers	NHEK	skin
44	chr6:128831200-128832600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr6:128831200-128835200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:128831400-128832200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:128831400-128832200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr6:128831400-128832400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:128831400-128832400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:128831400-128832400	Weak transcription	Duodenum Mucosa	Duodenum

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