Variant report

Variant	rs41280774
Chromosome Location	chr1:9789577-9789578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9778823..9786788-chr1:9787182..9791476,8	K562	blood:
2	chr1:9787700..9789917-chr1:9790535..9793046,2	K562	blood:
3	chr1:9776041..9778446-chr1:9788849..9791675,3	K562	blood:
4	chr1:9789064..9790899-chr1:9794257..9796422,2	K562	blood:
5	chr1:9788708..9790899-chr1:9794922..9796917,2	K562	blood:
6	chr1:9782219..9784206-chr1:9788877..9790888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171608	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11121485	0.81[EUR][1000 genomes]
rs11121486	0.81[EUR][1000 genomes]
rs11121488	0.81[EUR][1000 genomes]
rs1141402	0.91[EUR][1000 genomes]
rs12025864	0.91[EUR][1000 genomes]
rs12034313	0.91[EUR][1000 genomes]
rs12037599	0.91[EUR][1000 genomes]
rs12042293	0.81[EUR][1000 genomes]
rs41280776	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7550295	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh 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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9750600-9813000	Weak transcription	Right Atrium	heart
2	chr1:9777800-9790200	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:9777800-9790600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:9778400-9793400	Weak transcription	Fetal Kidney	kidney
5	chr1:9778600-9790600	Weak transcription	Small Intestine	intestine
6	chr1:9780000-9790800	Weak transcription	Hela-S3	cervix
7	chr1:9780600-9792600	Strong transcription	Dnd41	blood
8	chr1:9781200-9790200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:9781200-9813200	Strong transcription	Stomach Smooth Muscle	stomach
10	chr1:9781600-9800600	Weak transcription	Fetal Brain Male	brain
11	chr1:9781800-9793600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:9782200-9792800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:9783800-9789800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr1:9783800-9799600	Strong transcription	Fetal Brain Female	brain
15	chr1:9784000-9790600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:9784000-9793400	Strong transcription	Brain Germinal Matrix	brain
17	chr1:9784000-9797200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:9784000-9815400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:9784200-9792600	Strong transcription	Fetal Stomach	stomach
20	chr1:9784200-9796800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:9784200-9807400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:9784200-9815800	Strong transcription	Fetal Intestine Small	intestine
23	chr1:9784400-9790600	Strong transcription	Spleen	Spleen
24	chr1:9784400-9791400	Strong transcription	Fetal Intestine Large	intestine
25	chr1:9785200-9790200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:9785200-9792200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr1:9785800-9790000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:9786400-9792600	Strong transcription	GM12878-XiMat	blood
29	chr1:9786400-9792800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:9786400-9814000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:9786600-9793200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:9786600-9793400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:9786600-9798000	Strong transcription	Adipose Nuclei	Adipose
34	chr1:9786600-9802200	Strong transcription	Esophagus	oesophagus
35	chr1:9786600-9804800	Strong transcription	Ovary	ovary
36	chr1:9786600-9806000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:9786600-9807000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:9786600-9807000	Strong transcription	HepG2	liver
39	chr1:9786600-9815200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:9786800-9791000	Weak transcription	HUVEC	blood vessel
41	chr1:9786800-9793400	Strong transcription	Lung	lung
42	chr1:9786800-9793800	Strong transcription	NH-A	brain
43	chr1:9786800-9796000	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr1:9786800-9802600	Strong transcription	Osteobl	bone
45	chr1:9786800-9806200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr1:9786800-9807200	Strong transcription	Placenta	Placenta
47	chr1:9786800-9814000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:9787000-9789800	Genic enhancers	Fetal Thymus	thymus
49	chr1:9787000-9792800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:9787000-9793400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links