Variant report

Variant	rs2386227
Chromosome Location	chr4:8439771-8439772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8439008..8440667-chr4:8441503..8443852,2	K562	blood:
2	chr4:8429518..8431924-chr4:8437588..8440150,2	MCF-7	breast:
3	chr4:8439123..8440667-chr4:8441503..8443912,2	K562	blood:
4	chr4:8429704..8431761-chr4:8439023..8440743,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087008	Chromatin interaction
ENSG00000155275	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10461079	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1357481	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1543246	0.87[ASN][1000 genomes]
rs1880023	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1880024	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1916326	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1949733	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2010758	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2140337	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2450475	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2631731	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2631734	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2631735	0.96[CEU][hapmap];0.89[YRI][hapmap];0.96[EUR][1000 genomes]
rs2631736	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2631740	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2631742	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631743	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631744	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2631745	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631746	0.89[ASN][1000 genomes]
rs2631754	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631756	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2631758	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631762	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631768	0.83[EUR][1000 genomes]
rs2688219	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688223	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2688224	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688227	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688231	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688233	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2688235	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688242	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2688243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688247	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3103067	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3103069	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3103070	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3103071	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3103072	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3103099	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4696828	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6447875	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6837429	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6845969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6858542	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs868105	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs871768	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs940133	0.80[YRI][hapmap]
rs940134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs940136	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2386227	TRMT44	cis	Nerve Tibial	GTEx
rs2386227	RP11-689P11.2	cis	lung	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8430800-8441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:8430800-8441400	Weak transcription	Fetal Brain Female	brain
3	chr4:8430800-8441800	Weak transcription	Aorta	Aorta
4	chr4:8431000-8440600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:8431000-8441000	Weak transcription	A549	lung
6	chr4:8431000-8441200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:8431000-8441600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:8433800-8442000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:8435600-8441200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:8437800-8440200	Enhancers	Thymus	Thymus
11	chr4:8437800-8440600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:8437800-8441000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:8437800-8441200	Enhancers	Liver	Liver
14	chr4:8437800-8441400	Weak transcription	HSMM	muscle
15	chr4:8438000-8440800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:8438000-8441000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:8438000-8441400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr4:8438000-8441400	Weak transcription	NHDF-Ad	bronchial
19	chr4:8438000-8441800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:8438200-8439800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:8438200-8439800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:8438200-8440800	Weak transcription	Osteobl	bone
23	chr4:8438200-8441200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr4:8438200-8441200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:8438200-8441200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr4:8438200-8441400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:8438200-8441400	Weak transcription	Fetal Heart	heart
28	chr4:8438200-8441600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:8438200-8441600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:8438200-8441800	Weak transcription	Gastric	stomach
31	chr4:8438200-8442000	Weak transcription	Spleen	Spleen
32	chr4:8438400-8439800	Enhancers	GM12878-XiMat	blood
33	chr4:8438400-8440600	Weak transcription	Primary T cells from cord blood	blood
34	chr4:8438400-8440800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:8438400-8440800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr4:8438400-8441000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:8438400-8441200	Weak transcription	Primary B cells from cord blood	blood
38	chr4:8438400-8442000	Weak transcription	Small Intestine	intestine
39	chr4:8438800-8439800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr4:8438800-8440000	Enhancers	Placenta Amnion	Placenta Amnion
41	chr4:8439000-8439800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr4:8439000-8439800	Flanking Active TSS	Fetal Lung	lung
43	chr4:8439000-8439800	Enhancers	Fetal Stomach	stomach
44	chr4:8439000-8439800	Flanking Active TSS	NHEK	skin
45	chr4:8439000-8440000	Enhancers	Placenta	Placenta
46	chr4:8439000-8440400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:8439000-8441600	Enhancers	Brain Substantia Nigra	brain
48	chr4:8439000-8441800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:8439200-8439800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr4:8439200-8440000	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links