Variant report

Variant	rs59224049
Chromosome Location	chr4:102266190-102266191
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr4:102265923-102271471	SK-N-SH	brain:	n/a	n/a
2	GATA2	chr4:102266094-102267135	SH-SY5Y	brain:	n/a	chr4:102266408-102266417

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102265718..102267485-chr4:103187307..103189886,2	MCF-7	breast:
2	chr4:102263328..102265199-chr4:102265515..102267436,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EMCN-3	chr4:102265025-102267178	NONHSAT097571

Variant related genes	Relation type
ENSG00000254531	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1011849	0.92[AFR][1000 genomes]
rs1372243	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1372244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1441431	0.98[AFR][1000 genomes]
rs1561722	0.97[AFR][1000 genomes]
rs17031168	0.92[AFR][1000 genomes]
rs17031172	0.98[AFR][1000 genomes]
rs17031175	0.98[AFR][1000 genomes]
rs17031176	0.98[AFR][1000 genomes]
rs17031180	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17031182	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3789755	0.82[AFR][1000 genomes]
rs3974659	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4488940	0.88[AFR][1000 genomes]
rs4504259	0.88[AFR][1000 genomes]
rs4637408	0.92[AFR][1000 genomes]
rs55667372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58629361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59079781	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59763039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60438397	0.97[AFR][1000 genomes]
rs60984918	0.98[AFR][1000 genomes]
rs6532924	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6532925	0.98[AFR][1000 genomes]
rs6532926	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6810812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6812094	0.98[AFR][1000 genomes]
rs6817805	0.81[AFR][1000 genomes]
rs6827528	0.88[AFR][1000 genomes]
rs6828025	0.88[AFR][1000 genomes]
rs6830390	0.88[AFR][1000 genomes]
rs6831471	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6831824	0.81[AFR][1000 genomes]
rs6832020	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6834721	0.92[AFR][1000 genomes]
rs6837858	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6842191	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6844844	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6846554	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6852282	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835923	0.87[AFR][1000 genomes]
rs73835924	0.92[AFR][1000 genomes]
rs73835931	0.92[AFR][1000 genomes]
rs73835933	0.92[AFR][1000 genomes]
rs73835934	0.98[AFR][1000 genomes]
rs73835935	0.98[AFR][1000 genomes]
rs73835936	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835937	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835938	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835943	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835944	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7661895	0.98[AFR][1000 genomes]
rs7664396	0.98[AFR][1000 genomes]
rs7671524	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102249600-102266400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:102252800-102266400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:102254000-102266600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:102255200-102266400	Weak transcription	Gastric	stomach
5	chr4:102255400-102266600	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:102256800-102266200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:102257000-102266400	Weak transcription	Left Ventricle	heart
8	chr4:102257000-102266400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:102257000-102266400	Weak transcription	Right Ventricle	heart
10	chr4:102257000-102266400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:102257600-102266600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:102258000-102266200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:102258200-102266400	Weak transcription	Spleen	Spleen
14	chr4:102258800-102266400	Weak transcription	HSMM	muscle
15	chr4:102259000-102266400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:102259200-102266600	Weak transcription	Pancreas	Pancrea
17	chr4:102259400-102266200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:102260400-102266200	Weak transcription	Right Atrium	heart
19	chr4:102260400-102266400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:102260400-102266400	Weak transcription	Small Intestine	intestine
21	chr4:102261800-102266600	Weak transcription	Placenta	Placenta
22	chr4:102262800-102266200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:102263400-102266400	Enhancers	Brain Substantia Nigra	brain
24	chr4:102264000-102266400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:102264200-102266200	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr4:102264200-102266400	Weak transcription	Psoas Muscle	Psoas
27	chr4:102264400-102266200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:102264400-102266400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:102264600-102266200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:102264600-102266200	Weak transcription	Ovary	ovary
31	chr4:102264800-102266200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr4:102264800-102266200	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr4:102264800-102266400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:102264800-102266400	Enhancers	Dnd41	blood
35	chr4:102265000-102266200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:102265600-102266400	Enhancers	Primary T cells from cord blood	blood
37	chr4:102265600-102266400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:102265600-102266400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr4:102265600-102269800	Active TSS	NHLF	lung
40	chr4:102265800-102266200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:102265800-102266200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr4:102265800-102266200	Flanking Active TSS	A549	lung
43	chr4:102265800-102266400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:102265800-102266400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr4:102265800-102266400	Enhancers	Primary B cells from peripheral blood	blood
46	chr4:102265800-102266400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr4:102265800-102266400	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr4:102265800-102266400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr4:102265800-102266600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr4:102265800-102266600	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links