Variant report

Variant	rs2633438
Chromosome Location	chr1:154308508-154308509
allele	A/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154306397..154309276-chr1:154322045..154324098,3	MCF-7	breast:
2	chr1:154264672..154266840-chr1:154306843..154308967,2	MCF-7	breast:
3	chr1:154296733..154298208-chr1:154306834..154309045,12	MCF-7	breast:
4	chr1:154307761..154310261-chr1:154310334..154313311,3	K562	blood:
5	chr1:154307201..154309234-chr1:154310188..154312854,2	MCF-7	breast:
6	chr1:154307733..154310042-chr1:154313433..154315185,2	K562	blood:
7	chr1:154153078..154156691-chr1:154305231..154310554,8	MCF-7	breast:
8	chr1:154307075..154308806-chr2:174828188..174830288,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000238365	Chromatin interaction
ENSG00000172845	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11809740	0.83[ASN][1000 genomes]
rs1352333	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1626035	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1760796	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2274988	0.83[ASN][1000 genomes]
rs2481064	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2483710	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2483711	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2988721	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35463210	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154301400-154318400	Weak transcription	Small Intestine	intestine
2	chr1:154302200-154312200	Weak transcription	Gastric	stomach
3	chr1:154302200-154312600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:154302200-154322400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:154302400-154322400	Strong transcription	Dnd41	blood
6	chr1:154302400-154323200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:154302600-154309800	Weak transcription	Fetal Brain Male	brain
8	chr1:154302600-154314400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:154302600-154318200	Weak transcription	Fetal Heart	heart
10	chr1:154302600-154320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:154302600-154322600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:154302600-154323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:154302800-154323000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:154303000-154313000	Weak transcription	Colonic Mucosa	Colon
15	chr1:154303000-154322200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:154303000-154322600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:154303200-154312800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:154303200-154322200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:154303200-154322400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:154303200-154323400	Strong transcription	Fetal Brain Female	brain
21	chr1:154303200-154324600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:154303600-154308800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:154303800-154308800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:154304000-154322000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:154304200-154312600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:154304400-154312800	Weak transcription	Esophagus	oesophagus
27	chr1:154304600-154309800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:154304800-154309800	Weak transcription	Right Ventricle	heart
29	chr1:154304800-154312600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:154304800-154317800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:154305400-154309600	Weak transcription	GM12878-XiMat	blood
32	chr1:154305400-154311600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:154305800-154309200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:154305800-154322200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr1:154306000-154309600	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr1:154306000-154309800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr1:154306200-154314200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:154306400-154308800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:154306400-154310800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:154306400-154322400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:154306800-154312000	Weak transcription	HSMM	muscle
42	chr1:154307000-154309600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:154307000-154309600	Weak transcription	K562	blood
44	chr1:154307000-154309800	Weak transcription	Placenta	Placenta
45	chr1:154307200-154309600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:154307200-154309600	Weak transcription	Thymus	Thymus
47	chr1:154307200-154309800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:154307200-154311200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:154307200-154314600	Weak transcription	NHEK	skin
50	chr1:154307400-154309800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links