Variant report

Variant	rs2138867
Chromosome Location	chr4:48770546-48770547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48770305..48771971-chr4:48780871..48782395,2	K562	blood:
2	chr4:48768871..48771023-chr4:48775443..48777643,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10029425	1.00[AMR][1000 genomes]
rs10034207	1.00[AMR][1000 genomes]
rs10049760	1.00[AMR][1000 genomes]
rs10805171	1.00[AMR][1000 genomes]
rs10805172	1.00[AMR][1000 genomes]
rs10938535	1.00[AMR][1000 genomes]
rs10938538	1.00[AMR][1000 genomes]
rs10938539	1.00[AMR][1000 genomes]
rs10938541	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12500224	1.00[AMR][1000 genomes]
rs12500244	1.00[AMR][1000 genomes]
rs12507475	1.00[AMR][1000 genomes]
rs12507546	1.00[AMR][1000 genomes]
rs1474072	1.00[AMR][1000 genomes]
rs1517673	1.00[AMR][1000 genomes]
rs1517676	1.00[AMR][1000 genomes]
rs1517677	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1533511	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1554257	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1616561	1.00[AMR][1000 genomes]
rs1702796	1.00[AMR][1000 genomes]
rs1702799	1.00[AMR][1000 genomes]
rs1712771	1.00[AMR][1000 genomes]
rs1949422	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2138866	1.00[AMR][1000 genomes]
rs28371079	1.00[AMR][1000 genomes]
rs2883410	1.00[AMR][1000 genomes]
rs2940319	1.00[AMR][1000 genomes]
rs4235155	1.00[AMR][1000 genomes]
rs4235157	1.00[AMR][1000 genomes]
rs4330326	1.00[AMR][1000 genomes]
rs4558842	1.00[AMR][1000 genomes]
rs4694896	1.00[AMR][1000 genomes]
rs4694898	1.00[AMR][1000 genomes]
rs4694903	1.00[AMR][1000 genomes]
rs4695385	1.00[AMR][1000 genomes]
rs4695386	1.00[AMR][1000 genomes]
rs4695390	1.00[AMR][1000 genomes]
rs4695402	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4695403	1.00[AMR][1000 genomes]
rs4695405	1.00[AMR][1000 genomes]
rs6447642	1.00[AMR][1000 genomes]
rs6447654	1.00[AMR][1000 genomes]
rs6447656	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6447657	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6823351	1.00[AMR][1000 genomes]
rs6827481	1.00[AMR][1000 genomes]
rs6828500	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6835757	1.00[AMR][1000 genomes]
rs6844088	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6846797	1.00[AMR][1000 genomes]
rs6848222	1.00[AMR][1000 genomes]
rs6848417	1.00[AMR][1000 genomes]
rs6853876	1.00[AMR][1000 genomes]
rs707720	1.00[AMR][1000 genomes]
rs7434721	1.00[AMR][1000 genomes]
rs7664507	1.00[AMR][1000 genomes]
rs7689293	1.00[AMR][1000 genomes]
rs7689662	1.00[AMR][1000 genomes]
rs7692480	1.00[AMR][1000 genomes]
rs7698064	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs776581	1.00[AMR][1000 genomes]
rs776583	1.00[AMR][1000 genomes]
rs776587	1.00[AMR][1000 genomes]
rs776589	1.00[AMR][1000 genomes]
rs776595	1.00[AMR][1000 genomes]
rs776603	1.00[AMR][1000 genomes]
rs938789	0.81[AFR][1000 genomes]
rs938791	1.00[AMR][1000 genomes]
rs9994214	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998178	1.00[AMR][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	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48731600-48779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48747200-48777200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:48751600-48777200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:48754800-48774200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:48755000-48773600	Weak transcription	Aorta	Aorta
6	chr4:48755200-48774200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr4:48755400-48775600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:48755600-48774800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:48756000-48773000	Weak transcription	HUVEC	blood vessel
10	chr4:48756000-48774800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:48756200-48774200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:48759000-48775600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:48759000-48778600	Weak transcription	Fetal Stomach	stomach
14	chr4:48759200-48775400	Weak transcription	NHEK	skin
15	chr4:48759200-48775600	Weak transcription	HMEC	breast
16	chr4:48761000-48779800	Weak transcription	Placenta	Placenta
17	chr4:48762000-48775200	Weak transcription	Fetal Lung	lung
18	chr4:48762000-48777200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:48763000-48779800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:48764000-48775000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:48764200-48770800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:48764200-48773600	Weak transcription	Right Ventricle	heart
23	chr4:48764400-48773000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr4:48764600-48774400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:48764600-48779800	Weak transcription	HSMM	muscle
26	chr4:48764800-48773600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:48766000-48774800	Weak transcription	Dnd41	blood
28	chr4:48766600-48779800	Weak transcription	Ovary	ovary
29	chr4:48766800-48772000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr4:48767000-48779800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:48767200-48772000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:48767400-48770800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:48767400-48775600	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:48767800-48771800	Enhancers	Brain Hippocampus Middle	brain
35	chr4:48768000-48780800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:48768400-48771000	Weak transcription	Liver	Liver
37	chr4:48768600-48772800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:48768600-48773200	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:48768600-48773600	Weak transcription	Psoas Muscle	Psoas
40	chr4:48768600-48774800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:48768600-48774800	Weak transcription	Small Intestine	intestine
42	chr4:48768600-48775600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:48768600-48775600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:48768600-48775600	Weak transcription	Right Atrium	heart
45	chr4:48768600-48775600	Weak transcription	Spleen	Spleen
46	chr4:48768600-48777200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:48768600-48777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:48768600-48780000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr4:48768600-48780800	Weak transcription	Gastric	stomach
50	chr4:48768800-48771400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links