Variant report

Variant	rs2559523
Chromosome Location	chr10:22893246-22893247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:22891512..22893279-chr10:22903726..22905371,2	K562	blood:
2	chr10:22892740..22895922-chr10:23342638..23345686,4	K562	blood:
3	chr10:22878984..22881572-chr10:22891106..22893611,2	K562	blood:

Variant related genes	Relation type
ENSG00000150867	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10159847	0.83[GIH][hapmap]
rs1062190	1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs10764338	1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs10828320	0.81[TSI][hapmap]
rs11013104	0.84[CHD][hapmap]
rs11013110	0.88[JPT][hapmap]
rs1171505	0.88[JPT][hapmap]
rs12254366	1.00[ASN][1000 genomes]
rs12261508	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1326338	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1359642	0.83[ASN][1000 genomes]
rs1409397	0.89[JPT][hapmap]
rs1631873	0.87[GIH][hapmap]
rs16922479	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1750750	0.89[JPT][hapmap]
rs1750752	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1750754	0.89[JPT][hapmap]
rs1750757	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1750759	0.81[EUR][1000 genomes]
rs1750760	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1750770	0.86[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap]
rs1778302	0.95[GIH][hapmap];0.91[TSI][hapmap]
rs1778317	0.91[GIH][hapmap]
rs1778331	0.89[JPT][hapmap]
rs1778351	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778352	0.82[EUR][1000 genomes]
rs1778353	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs1778355	0.89[JPT][hapmap]
rs1778356	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256542	0.88[AFR][1000 genomes]
rs2559520	0.95[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2559522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2559524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2559526	0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2559527	0.89[JPT][hapmap]
rs2559528	0.86[JPT][hapmap];0.82[AFR][1000 genomes]
rs2559529	0.91[GIH][hapmap];0.91[TSI][hapmap]
rs2765993	0.95[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs2765994	0.89[JPT][hapmap]
rs2765995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765996	0.91[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2765998	0.81[AFR][1000 genomes]
rs2798982	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2913109	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2913110	0.89[JPT][hapmap];0.80[YRI][hapmap]
rs7094187	0.88[JPT][hapmap]
rs7095020	0.88[JPT][hapmap]
rs7098460	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7099314	0.89[JPT][hapmap];0.80[YRI][hapmap]
rs754822	0.89[JPT][hapmap]
rs7907744	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs7912144	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7916957	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830947	chr10:22881196-23004381	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22844200-22904800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:22856600-22899200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr10:22858200-22904000	Weak transcription	Colonic Mucosa	Colon
4	chr10:22862400-22902000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:22866600-22893800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:22870200-22893400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:22870400-22895200	Weak transcription	HepG2	liver
8	chr10:22877200-22896400	Weak transcription	Fetal Intestine Large	intestine
9	chr10:22877600-22893400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr10:22879000-22894000	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr10:22880000-22906800	Weak transcription	Colon Smooth Muscle	Colon
12	chr10:22880200-22893400	Weak transcription	Ovary	ovary
13	chr10:22880200-22893800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr10:22880200-22895200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr10:22880200-22896200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:22880200-22897000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr10:22880400-22896600	Weak transcription	Liver	Liver
18	chr10:22880600-22893600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:22881800-22893400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr10:22883200-22893800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr10:22883200-22894000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr10:22883200-22896200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr10:22883200-22899200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr10:22885200-22894000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr10:22885200-22896200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr10:22886200-22893800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr10:22886400-22894600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:22886600-22896800	Weak transcription	HSMMtube	muscle
29	chr10:22887000-22894200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr10:22887200-22902400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr10:22888600-22893600	Weak transcription	Small Intestine	intestine
32	chr10:22888600-22893800	Weak transcription	HMEC	breast
33	chr10:22888600-22895000	Weak transcription	Placenta	Placenta
34	chr10:22888800-22893600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:22888800-22893800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr10:22888800-22893800	Weak transcription	NHEK	skin
37	chr10:22888800-22895200	Weak transcription	A549	lung
38	chr10:22888800-22898000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr10:22888800-22905000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr10:22889000-22893600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr10:22889000-22893800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr10:22889000-22893800	Weak transcription	NH-A	brain
43	chr10:22889000-22894000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr10:22889000-22894000	Weak transcription	Osteobl	bone
45	chr10:22889000-22895400	Weak transcription	K562	blood
46	chr10:22889000-22896800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr10:22889400-22893400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:22889400-22904400	Weak transcription	Hela-S3	cervix
49	chr10:22889800-22893400	Weak transcription	NHDF-Ad	bronchial
50	chr10:22889800-22894200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links