Variant report

Variant	rs6844088
Chromosome Location	chr4:48783698-48783699
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr4:48783685-48783961	HepG2	liver:	n/a	n/a
2	FOXA2	chr4:48783563-48783755	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:48564315..48567259-chr4:48782772..48784817,2	K562	blood:
2	chr4:48780694..48783941-chr4:48830567..48835952,11	MCF-7	breast:
3	chr4:48782469..48785403-chr4:48787452..48790375,2	MCF-7	breast:
4	chr4:48783390..48785837-chr4:48789039..48791747,3	K562	blood:
5	chr4:48783503..48785645-chr4:48863021..48865080,2	MCF-7	breast:
6	chr4:48781641..48784567-chr4:48855819..48858602,2	MCF-7	breast:

No data

Variant related genes	Relation type
FRYL	TF binding region
ENSG00000109180	Chromatin interaction
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

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	0.80[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	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1533511	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1554257	0.80[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	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2138866	1.00[AMR][1000 genomes]
rs2138867	0.82[AFR][1000 genomes];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]
rs6447654	1.00[AMR][1000 genomes]
rs6447656	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6447657	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6823351	1.00[AMR][1000 genomes]
rs6827481	1.00[AMR][1000 genomes]
rs6828500	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6835757	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]
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	0.98[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]
rs938791	1.00[AMR][1000 genomes]
rs9994214	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998178	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48780000-48783800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr4:48780400-48783800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr4:48780600-48783800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr4:48780800-48783800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:48783000-48783800	Flanking Active TSS	NHEK	skin
6	chr4:48783200-48783800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:48783200-48783800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:48783200-48783800	Flanking Active TSS	Fetal Kidney	kidney
9	chr4:48783400-48783800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr4:48783400-48783800	Enhancers	Primary B cells from cord blood	blood
11	chr4:48783400-48783800	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr4:48783400-48783800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:48783400-48783800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:48783400-48783800	Enhancers	Colon Smooth Muscle	Colon
15	chr4:48783400-48783800	Enhancers	Fetal Heart	heart
16	chr4:48783400-48783800	Enhancers	Fetal Intestine Small	intestine
17	chr4:48783400-48783800	Enhancers	Fetal Thymus	thymus
18	chr4:48783400-48783800	Enhancers	K562	blood
19	chr4:48783400-48784000	Enhancers	Fetal Intestine Large	intestine
20	chr4:48783400-48788600	Weak transcription	Brain Angular Gyrus	brain
21	chr4:48783600-48783800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr4:48783600-48783800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr4:48783600-48783800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:48783600-48783800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:48783600-48783800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr4:48783600-48783800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr4:48783600-48783800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr4:48783600-48783800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:48783600-48783800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr4:48783600-48783800	Enhancers	Primary hematopoietic stem cells	blood
31	chr4:48783600-48783800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:48783600-48783800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr4:48783600-48783800	Enhancers	Brain Hippocampus Middle	brain
34	chr4:48783600-48783800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr4:48783600-48783800	Enhancers	Brain Substantia Nigra	brain
36	chr4:48783600-48783800	Enhancers	Colonic Mucosa	Colon
37	chr4:48783600-48783800	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr4:48783600-48783800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr4:48783600-48783800	Enhancers	Fetal Brain Male	brain
40	chr4:48783600-48783800	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr4:48783600-48783800	Enhancers	GM12878-XiMat	blood
42	chr4:48783600-48783800	Enhancers	Hela-S3	cervix
43	chr4:48783600-48784000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr4:48783600-48784000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:48783600-48784000	Enhancers	Dnd41	blood
46	chr4:48783600-48784000	Flanking Active TSS	HepG2	liver
47	chr4:48783600-48784200	Enhancers	Brain Cingulate Gyrus	brain
48	chr4:48783600-48784200	Enhancers	HMEC	breast
49	chr4:48783600-48784400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr4:48783600-48784400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links