Variant report

Variant	rs2858223
Chromosome Location	chr22:33019789-33019790
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:33014781..33017660-chr22:33019637..33021375,2	MCF-7	breast:
2	chr22:33016718..33020351-chr22:33021844..33025503,4	K562	blood:
3	chr22:33015941..33022634-chr22:33022783..33027992,6	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16990857	0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs16990872	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2051569	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs2157168	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs3827336	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs5749471	0.85[CEU][hapmap]
rs58228617	0.89[ASN][1000 genomes]
rs58291507	0.89[ASN][1000 genomes]
rs58410126	0.89[ASN][1000 genomes]
rs8135117	0.86[JPT][hapmap]
rs9609603	0.86[JPT][hapmap]
rs9609608	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs9619283	0.86[JPT][hapmap]
rs9621513	0.86[JPT][hapmap]
rs9621515	0.85[JPT][hapmap]
rs988670	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055541	chr22:33006967-33101138	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2762119	chr22:33006967-33101150	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1061824	chr22:33013014-33101138	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2858223	XBP1	cis	parietal	SCAN
rs2858223	DRG1	cis	cerebellum	SCAN
rs2858223	OSM	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33014200-33022200	Weak transcription	Small Intestine	intestine
2	chr22:33014400-33019800	Weak transcription	Brain Angular Gyrus	brain
3	chr22:33015000-33019800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr22:33016000-33020000	Weak transcription	Liver	Liver
5	chr22:33017000-33020200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:33017000-33020600	Enhancers	Fetal Kidney	kidney
7	chr22:33017000-33021000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr22:33017000-33021000	Enhancers	Fetal Muscle Leg	muscle
9	chr22:33017000-33021000	Enhancers	Fetal Stomach	stomach
10	chr22:33017000-33022600	Enhancers	Fetal Lung	lung
11	chr22:33017000-33022600	Enhancers	Right Atrium	heart
12	chr22:33017000-33025800	Enhancers	Left Ventricle	heart
13	chr22:33017000-33025800	Enhancers	Spleen	Spleen
14	chr22:33017000-33027200	Enhancers	Placenta	Placenta
15	chr22:33017200-33020600	Enhancers	Colon Smooth Muscle	Colon
16	chr22:33017200-33020800	Enhancers	Ovary	ovary
17	chr22:33017400-33020000	Enhancers	Fetal Heart	heart
18	chr22:33017400-33020600	Enhancers	Colonic Mucosa	Colon
19	chr22:33017400-33020600	Enhancers	Right Ventricle	heart
20	chr22:33017400-33020600	Enhancers	NHLF	lung
21	chr22:33017400-33021000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr22:33017600-33019800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr22:33017600-33020000	Enhancers	Rectal Smooth Muscle	rectum
24	chr22:33017600-33020200	Enhancers	Fetal Intestine Small	intestine
25	chr22:33017600-33020400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr22:33017600-33020400	Enhancers	Brain Hippocampus Middle	brain
27	chr22:33017800-33020200	Enhancers	Brain Substantia Nigra	brain
28	chr22:33017800-33020400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr22:33017800-33020400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr22:33017800-33020400	Enhancers	HSMM	muscle
31	chr22:33017800-33020600	Enhancers	Osteobl	bone
32	chr22:33017800-33020800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr22:33017800-33022200	Weak transcription	Psoas Muscle	Psoas
34	chr22:33017800-33022200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr22:33018200-33020600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr22:33018400-33021000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr22:33018400-33025800	Enhancers	Adipose Nuclei	Adipose
38	chr22:33018600-33020000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:33018600-33020000	Enhancers	HSMMtube	muscle
40	chr22:33018600-33020400	Enhancers	NH-A	brain
41	chr22:33018600-33020400	Enhancers	NHDF-Ad	bronchial
42	chr22:33018600-33020800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr22:33018600-33020800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr22:33018600-33021400	Enhancers	Fetal Muscle Trunk	muscle
45	chr22:33018600-33021400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr22:33018600-33023800	Enhancers	Hela-S3	cervix
47	chr22:33019000-33019800	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr22:33019000-33019800	Enhancers	Stomach Smooth Muscle	stomach
49	chr22:33019000-33020600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr22:33019000-33022200	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links