Variant report

Variant	rs4988680
Chromosome Location	chr1:9799852-9799853
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9799251..9800948-chr1:9805538..9808138,2	K562	blood:
2	chr1:9795106..9799024-chr1:9799834..9803861,3	K562	blood:

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

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

rs_ID	r²[population]
rs58978222	1.00[AMR][1000 genomes]
rs6664451	1.00[AMR][1000 genomes]
rs72855710	1.00[AMR][1000 genomes]
rs72855712	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72855717	1.00[AMR][1000 genomes]
rs72855750	1.00[AMR][1000 genomes]
rs72871215	1.00[AMR][1000 genomes]
rs72871220	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72871223	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72871231	1.00[AFR][1000 genomes];1.00[AMR][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:126 , 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	chr1:9781200-9813200	Strong transcription	Stomach Smooth Muscle	stomach
3	chr1:9781600-9800600	Weak transcription	Fetal Brain Male	brain
4	chr1:9784000-9815400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:9784200-9807400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:9784200-9815800	Strong transcription	Fetal Intestine Small	intestine
7	chr1:9786400-9814000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:9786600-9802200	Strong transcription	Esophagus	oesophagus
9	chr1:9786600-9804800	Strong transcription	Ovary	ovary
10	chr1:9786600-9806000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:9786600-9807000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:9786600-9807000	Strong transcription	HepG2	liver
13	chr1:9786600-9815200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:9786800-9802600	Strong transcription	Osteobl	bone
15	chr1:9786800-9806200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr1:9786800-9807200	Strong transcription	Placenta	Placenta
17	chr1:9786800-9814000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:9787000-9801600	Strong transcription	Gastric	stomach
19	chr1:9787000-9801600	Strong transcription	Right Ventricle	heart
20	chr1:9787000-9805600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:9787000-9807000	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr1:9787000-9813000	Weak transcription	Fetal Heart	heart
23	chr1:9787200-9802400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:9787200-9804800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:9787200-9806800	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:9787200-9807200	Strong transcription	Fetal Muscle Leg	muscle
27	chr1:9787400-9801800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:9787400-9806400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:9787400-9807000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:9787400-9807200	Strong transcription	Left Ventricle	heart
31	chr1:9787400-9807200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:9787400-9811800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:9787600-9802200	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:9787600-9807400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:9787600-9812000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:9787600-9813200	Strong transcription	Fetal Muscle Trunk	muscle
37	chr1:9787600-9815200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr1:9788000-9802400	Strong transcription	Brain Hippocampus Middle	brain
39	chr1:9788000-9807000	Strong transcription	NHEK	skin
40	chr1:9788200-9804800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:9788400-9807400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:9788400-9811800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:9788600-9801800	Strong transcription	Brain Substantia Nigra	brain
44	chr1:9789400-9802400	Strong transcription	Colon Smooth Muscle	Colon
45	chr1:9789800-9815400	Strong transcription	Fetal Thymus	thymus
46	chr1:9789800-9815800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:9790000-9800600	Weak transcription	Psoas Muscle	Psoas
48	chr1:9790600-9805000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:9790600-9815400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:9791600-9814200	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links