Variant report

Variant	rs2092054
Chromosome Location	chr22:28383549-28383550
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr22:28382335-28384048	IMR90	lung:	n/a	n/a
2	TEAD4	chr22:28383430-28383739	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr22:28383493-28383851	IMR90	lung:	n/a	n/a
4	POLR2A	chr22:28383446-28383567	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28382655..28384335-chr22:28385888..28387881,2	MCF-7	breast:

Variant related genes	Relation type
TTC28-AS1	TF binding region
ENSG00000100154	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs118839	0.89[ASN][1000 genomes]
rs12171034	0.84[ASN][1000 genomes]
rs138631	0.85[ASN][1000 genomes]
rs138638	0.93[ASN][1000 genomes]
rs138650	0.92[ASN][1000 genomes]
rs138675	0.84[ASN][1000 genomes]
rs138683	0.87[ASN][1000 genomes]
rs138685	0.81[ASN][1000 genomes]
rs1548235	0.83[ASN][1000 genomes]
rs2038158	0.85[ASN][1000 genomes]
rs3747141	0.87[ASN][1000 genomes]
rs4140571	0.91[ASN][1000 genomes]
rs470100	0.89[ASN][1000 genomes]
rs470105	0.84[ASN][1000 genomes]
rs5752667	0.82[ASN][1000 genomes]
rs73425788	0.81[ASN][1000 genomes]
rs7625	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv522306	chr22:28378472-28402624	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28355400-28387800	Weak transcription	Fetal Brain Male	brain
2	chr22:28360800-28392400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr22:28368800-28385800	Weak transcription	Brain Angular Gyrus	brain
4	chr22:28369200-28398400	Weak transcription	Hela-S3	cervix
5	chr22:28369400-28394000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr22:28370400-28387200	Weak transcription	Fetal Kidney	kidney
7	chr22:28371800-28386800	Weak transcription	NHDF-Ad	bronchial
8	chr22:28371800-28395000	Weak transcription	Small Intestine	intestine
9	chr22:28372000-28386400	Weak transcription	HUVEC	blood vessel
10	chr22:28373600-28404000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:28373800-28386400	Strong transcription	Fetal Muscle Leg	muscle
12	chr22:28373800-28398200	Strong transcription	Fetal Brain Female	brain
13	chr22:28373800-28404200	Strong transcription	Fetal Stomach	stomach
14	chr22:28373800-28405200	Strong transcription	Fetal Intestine Small	intestine
15	chr22:28374600-28386400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr22:28376400-28383800	Strong transcription	Ovary	ovary
17	chr22:28376800-28383600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr22:28377200-28385800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr22:28377200-28386400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr22:28377200-28386800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr22:28377200-28386800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr22:28377200-28387200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr22:28377200-28388600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr22:28377800-28386400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr22:28377800-28386800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr22:28377800-28391800	Strong transcription	Fetal Lung	lung
27	chr22:28377800-28398000	Strong transcription	Fetal Intestine Large	intestine
28	chr22:28377800-28398600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr22:28378000-28384000	Strong transcription	Adipose Nuclei	Adipose
30	chr22:28378000-28386000	Strong transcription	Lung	lung
31	chr22:28378000-28396600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr22:28379000-28387600	Weak transcription	Thymus	Thymus
33	chr22:28379400-28383600	Strong transcription	Rectal Smooth Muscle	rectum
34	chr22:28379400-28399600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr22:28379600-28387000	Weak transcription	Colon Smooth Muscle	Colon
36	chr22:28379800-28388200	Weak transcription	Colonic Mucosa	Colon
37	chr22:28380200-28390400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr22:28380600-28383800	Strong transcription	Spleen	Spleen
39	chr22:28380600-28387200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr22:28380800-28383600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr22:28381000-28383800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr22:28381000-28388200	Weak transcription	Esophagus	oesophagus
43	chr22:28381200-28383600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr22:28381400-28388200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr22:28381600-28384800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr22:28381600-28384800	Weak transcription	Left Ventricle	heart
47	chr22:28381600-28384800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr22:28381600-28385800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr22:28381600-28393800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr22:28381800-28383600	Enhancers	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links