Variant report

Variant	rs4928120
Chromosome Location	chr3:99987017-99987018
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99978428..99981467-chr3:99986492..99990866,6	K562	blood:
2	chr3:99981876..99985966-chr3:99986124..99992664,8	K562	blood:
3	chr3:99985781..99987839-chr3:100119283..100121257,2	K562	blood:

Variant related genes	Relation type
ENSG00000154174	Chromatin interaction
ENSG00000206535	Chromatin interaction
ENSG00000036054	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10936193	1.00[LWK][hapmap]
rs11923373	0.90[JPT][hapmap]
rs12486660	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs17213695	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs17279479	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17315194	1.00[LWK][hapmap]
rs17335566	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs17335614	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs34748137	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4928166	0.90[JPT][hapmap]
rs4928170	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs62281674	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6800438	0.90[JPT][hapmap];0.85[MEX][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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4928120	TBC1D23	cis	cerebellum	SCAN
rs4928120	COL8A1	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-99988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:99980600-100037200	Weak transcription	Spleen	Spleen
3	chr3:99980600-100053200	Weak transcription	Gastric	stomach
4	chr3:99980800-99988800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:99981000-99990400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:99981000-99996400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:99981200-99988600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:99981200-99988800	Weak transcription	Fetal Brain Female	brain
9	chr3:99981200-99993200	Weak transcription	Primary B cells from cord blood	blood
10	chr3:99981200-99995400	Weak transcription	Brain Angular Gyrus	brain
11	chr3:99981200-99997800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr3:99981200-99998400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:99981200-99998600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:99981200-99998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:99981200-100004800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:99981200-100030800	Weak transcription	Fetal Heart	heart
17	chr3:99981400-99988600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:99981400-99998400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:99981400-100004400	Weak transcription	Lung	lung
20	chr3:99982200-99990400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:99982400-100005400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:99982600-99998800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:99982800-99987200	Weak transcription	Aorta	Aorta
24	chr3:99982800-100001400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:99983000-99987200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:99983000-99987200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:99983000-99988600	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:99983000-99990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:99983000-99995400	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:99983200-99987200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:99983200-99988000	Weak transcription	Ovary	ovary
32	chr3:99983200-99988200	Weak transcription	Fetal Brain Male	brain
33	chr3:99983200-99988600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:99983200-99988600	Weak transcription	Small Intestine	intestine
35	chr3:99983200-99999600	Weak transcription	Fetal Intestine Large	intestine
36	chr3:99983200-100010000	Weak transcription	Pancreas	Pancrea
37	chr3:99983400-99987400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:99983400-99988400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:99983400-99999400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:99984200-99987400	Weak transcription	Hela-S3	cervix
41	chr3:99984200-99987600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:99984200-99987600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:99984200-99988200	Enhancers	NHEK	skin
44	chr3:99984200-99988600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:99984200-99988600	Weak transcription	Stomach Mucosa	stomach
46	chr3:99984200-99993000	Weak transcription	GM12878-XiMat	blood
47	chr3:99984200-99998200	Weak transcription	Primary T cells from cord blood	blood
48	chr3:99984200-99998800	Weak transcription	Fetal Intestine Small	intestine
49	chr3:99984200-99999000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:99984200-99999400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links