Variant report

Variant	rs2010758
Chromosome Location	chr4:8475623-8475624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8472049..8473735-chr4:8474244..8476711,2	K562	blood:
2	chr4:8471024..8473735-chr4:8474244..8476611,2	K562	blood:
3	chr4:8475299..8477901-chr4:8499421..8502393,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155275	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10461079	0.81[ASN][1000 genomes]
rs1357481	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1543246	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1880023	0.98[ASN][1000 genomes]
rs1880024	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1916326	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1949733	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2140337	0.91[ASN][1000 genomes]
rs2386227	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2450475	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2631731	0.87[ASN][1000 genomes]
rs2631734	0.89[ASN][1000 genomes]
rs2631735	0.83[EUR][1000 genomes]
rs2631736	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631740	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2631742	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631743	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2631744	0.91[ASN][1000 genomes]
rs2631745	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2631746	0.93[ASN][1000 genomes]
rs2631754	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631756	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2631758	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2631762	0.89[ASN][1000 genomes]
rs2688219	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688223	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2688224	0.82[ASN][1000 genomes]
rs2688227	0.89[ASN][1000 genomes]
rs2688231	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2688233	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2688235	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688242	0.80[ASN][1000 genomes]
rs2688243	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2688247	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3103067	0.87[ASN][1000 genomes]
rs3103069	0.89[ASN][1000 genomes]
rs3103070	0.90[ASN][1000 genomes]
rs3103071	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3103072	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3103099	0.85[ASN][1000 genomes]
rs4696828	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6447875	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6837429	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6845969	0.81[ASN][1000 genomes]
rs6858542	0.86[ASN][1000 genomes]
rs868105	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs871768	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs940134	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs940136	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2010758	TRMT44	cis	Nerve Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8447000-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:8447200-8480200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:8447400-8482200	Strong transcription	Primary T cells from cord blood	blood
4	chr4:8459800-8478800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:8463800-8478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:8465200-8482200	Strong transcription	Brain Germinal Matrix	brain
7	chr4:8465400-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:8467600-8475800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:8467600-8482200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:8467800-8480400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:8468000-8478600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:8468400-8479600	Weak transcription	Psoas Muscle	Psoas
13	chr4:8470600-8479000	Weak transcription	Fetal Brain Male	brain
14	chr4:8471200-8476800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr4:8471200-8477400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:8471200-8480600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:8471400-8477200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:8471400-8477400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:8471400-8477400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:8471400-8479600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:8471400-8480200	Weak transcription	HMEC	breast
22	chr4:8471600-8477200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:8471600-8477800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:8471800-8477200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:8471800-8477600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:8471800-8477600	Weak transcription	A549	lung
27	chr4:8471800-8479600	Weak transcription	NHEK	skin
28	chr4:8471800-8480000	Weak transcription	GM12878-XiMat	blood
29	chr4:8471800-8480800	Weak transcription	HepG2	liver
30	chr4:8471800-8483200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr4:8472000-8477000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:8472000-8480200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr4:8472200-8477400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:8472200-8480800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:8472400-8477400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr4:8472400-8479800	Weak transcription	Primary B cells from cord blood	blood
37	chr4:8472600-8480000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:8472800-8476200	Weak transcription	Liver	Liver
39	chr4:8472800-8476800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:8473200-8476200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:8473200-8476400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:8473200-8477000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr4:8473400-8476200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr4:8473400-8476200	Enhancers	NHDF-Ad	bronchial
45	chr4:8473400-8476400	Enhancers	Placenta Amnion	Placenta Amnion
46	chr4:8473400-8476600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:8473400-8477000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr4:8473400-8477200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:8473400-8477200	Weak transcription	Dnd41	blood
50	chr4:8473400-8477600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links