Variant report

Variant	rs2488408
Chromosome Location	chr1:197644052-197644053
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	chr1:197637854..197639785-chr1:197643428..197645113,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10801618	0.81[AFR][1000 genomes]
rs1421392	1.00[AMR][1000 genomes]
rs2111933	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2477064	1.00[AMR][1000 genomes]
rs2477068	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3861932	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4382756	1.00[AMR][1000 genomes]
rs4915553	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6679357	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6692898	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7553626	1.00[AMR][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	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv548872	chr1:197529218-197644581	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv437263	chr1:197599030-197722240	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv873077	chr1:197615391-197698103	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197596600-197644800	Weak transcription	Ovary	ovary
2	chr1:197603200-197645000	Weak transcription	Esophagus	oesophagus
3	chr1:197611800-197644800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr1:197612800-197644800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:197612800-197645000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:197628800-197645000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:197629000-197644600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:197629000-197645000	Weak transcription	Dnd41	blood
9	chr1:197629000-197645200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:197633800-197644600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:197638000-197644600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:197638600-197644600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:197640200-197644400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:197640600-197644600	Weak transcription	K562	blood
15	chr1:197640800-197644200	Enhancers	Liver	Liver
16	chr1:197640800-197644400	Weak transcription	Osteobl	bone
17	chr1:197640800-197644800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:197640800-197644800	Weak transcription	Fetal Intestine Small	intestine
19	chr1:197640800-197647000	Weak transcription	Small Intestine	intestine
20	chr1:197640800-197657600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:197641800-197644600	Weak transcription	A549	lung
22	chr1:197641800-197645000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:197642000-197644600	Enhancers	Fetal Lung	lung
24	chr1:197642800-197644200	Weak transcription	Fetal Brain Male	brain
25	chr1:197642800-197645400	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr1:197642800-197645800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:197642800-197646800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:197643000-197644400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:197643200-197644200	Weak transcription	Fetal Brain Female	brain
30	chr1:197643200-197645600	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr1:197643400-197644200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:197643400-197644400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:197643400-197645400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:197643600-197644600	Weak transcription	Right Atrium	heart
35	chr1:197643600-197644600	Enhancers	NHDF-Ad	bronchial
36	chr1:197643600-197645000	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:197643600-197645000	Weak transcription	Pancreas	Pancrea
38	chr1:197643800-197646800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:197644000-197644400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:197644000-197644400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:197644000-197644800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:197644000-197645000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:197644000-197645000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:197644000-197656000	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links