Variant report

Variant	rs59048598
Chromosome Location	chr2:85848540-85848541
allele	A/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	SP1	chr2:85848381-85848857	HepG2	liver:	n/a	n/a
2	FOXA1	chr2:85848394-85848780	HepG2	liver:	n/a	n/a
3	TCF12	chr2:85848408-85848713	HepG2	liver:	n/a	n/a
4	FOXA1	chr2:85848290-85848936	HepG2	liver:	n/a	n/a
5	HEY1	chr2:85848237-85848807	HepG2	liver:	n/a	n/a
6	HNF4A	chr2:85848411-85848753	HepG2	liver:	n/a	chr2:85848614-85848629
7	HNF4A	chr2:85848404-85848813	HepG2	liver:	n/a	chr2:85848614-85848629
8	FOXA1	chr2:85848386-85848887	HepG2	liver:	n/a	n/a
9	FOXA2	chr2:85848459-85848769	HepG2	liver:	n/a	n/a
10	NFIC	chr2:85848373-85848875	HepG2	liver:	n/a	n/a
11	FOXA1	chr2:85848334-85848887	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:85847247..85848767-chr2:85853795..85856664,2	K562	blood:
2	chr2:85764998..85766948-chr2:85847415..85849726,2	MCF-7	breast:
3	chr2:85848190..85850227-chr2:85850662..85852884,2	K562	blood:
4	chr2:85843172..85845953-chr2:85846983..85848551,2	MCF-7	breast:

Variant related genes	Relation type
USP39	TF binding region
ENSG00000168906	Chromatin interaction
ENSG00000168883	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs3024803	0.87[AMR][1000 genomes]
rs3024805	0.87[AMR][1000 genomes]
rs3024810	0.87[AMR][1000 genomes]
rs3024811	0.87[AMR][1000 genomes]
rs3024815	1.00[AMR][1000 genomes]
rs3024818	1.00[AMR][1000 genomes]
rs3024819	1.00[AMR][1000 genomes]
rs3024822	1.00[AMR][1000 genomes]
rs3024827	1.00[AMR][1000 genomes]
rs3024828	1.00[AMR][1000 genomes]
rs4416212	0.91[AFR][1000 genomes]
rs57175088	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57762218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57789237	0.87[AMR][1000 genomes]
rs59139634	0.90[AFR][1000 genomes]
rs59227664	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60661938	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60755293	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60801683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61535370	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61536745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6547627	1.00[ASN][1000 genomes]
rs6718028	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72923051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923062	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923064	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923077	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923080	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923082	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7564769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7579847	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7580358	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7584055	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7589436	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7599812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85843800-85876000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:85844400-85850800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:85844800-85858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:85844800-85862600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:85844800-85881600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:85845000-85849200	Weak transcription	Pancreas	Pancrea
7	chr2:85845000-85849800	Weak transcription	Fetal Kidney	kidney
8	chr2:85845000-85850000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:85845000-85850600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:85845000-85850800	Weak transcription	Fetal Heart	heart
11	chr2:85845000-85850800	Weak transcription	Stomach Mucosa	stomach
12	chr2:85845000-85852800	Strong transcription	HSMM	muscle
13	chr2:85845000-85876000	Weak transcription	Right Atrium	heart
14	chr2:85845000-85879800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:85845000-85880000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:85845000-85880800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:85845000-85881400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:85845000-85881800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:85845000-85883600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:85845200-85855600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:85845400-85849600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:85845400-85853800	Strong transcription	K562	blood
23	chr2:85845400-85864600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:85845400-85879800	Strong transcription	Lung	lung
25	chr2:85845400-85881000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:85845400-85881400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:85845400-85886400	Strong transcription	Fetal Muscle Leg	muscle
28	chr2:85845600-85881800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:85845600-85882200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr2:85845800-85860800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr2:85845800-85865000	Strong transcription	NH-A	brain
32	chr2:85845800-85881400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:85845800-85881600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:85845800-85881800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:85846000-85848600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:85846000-85853600	Strong transcription	HUVEC	blood vessel
37	chr2:85846000-85856600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:85846000-85856600	Strong transcription	Spleen	Spleen
39	chr2:85846000-85875600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr2:85846000-85880800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:85846000-85881400	Strong transcription	Fetal Stomach	stomach
42	chr2:85846000-85881400	Strong transcription	Fetal Thymus	thymus
43	chr2:85846000-85887000	Strong transcription	Liver	Liver
44	chr2:85846000-85887400	Strong transcription	Fetal Intestine Small	intestine
45	chr2:85846200-85850800	Strong transcription	Left Ventricle	heart
46	chr2:85846200-85855600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:85846200-85864200	Strong transcription	Brain Germinal Matrix	brain
48	chr2:85846200-85871600	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:85846200-85874600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr2:85846200-85874600	Strong transcription	Monocytes-CD14+_RO01746	blood

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