Variant report

Variant	rs72887686
Chromosome Location	chr2:48568905-48568906
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr2:48568784-48569236	A549	lung:	n/a	n/a
2	NR3C1	chr2:48568674-48569177	A549	lung:	n/a	n/a
3	MAX	chr2:48568756-48568942	NB4	blood:	n/a	n/a
4	NR3C1	chr2:48568660-48569198	A549	lung:	n/a	n/a
5	NR3C1	chr2:48568662-48569213	A549	lung:	n/a	n/a
6	POLR2A	chr2:48568650-48569103	HepG2	liver:	n/a	n/a
7	FOXA1	chr2:48568708-48569247	A549	lung:	n/a	n/a
8	NR3C1	chr2:48568844-48569143	A549	lung:	n/a	n/a
9	USF1	chr2:48568652-48569025	A549	lung:	n/a	n/a
10	NR3C1	chr2:48568716-48569124	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48568069..48570400-chr2:48600787..48602390,2	K562	blood:
2	chr2:48568770..48570498-chr2:48574091..48575734,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNU4-49P	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs17037271	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28399967	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28439229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28485447	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28570232	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595126	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34136171	0.85[EUR][1000 genomes]
rs56879885	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57729372	0.84[AFR][1000 genomes]
rs60527991	0.82[AFR][1000 genomes]
rs60743061	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62137000	0.91[AFR][1000 genomes]
rs62138796	0.82[AFR][1000 genomes]
rs62138798	0.83[AFR][1000 genomes]
rs62138817	0.88[AFR][1000 genomes]
rs6545031	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545033	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6737455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72887650	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7563625	0.89[AFR][1000 genomes]
rs7576648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7583112	0.82[AFR][1000 genomes]
rs9677579	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48543600-48570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:48544400-48570400	Weak transcription	NHEK	skin
3	chr2:48544400-48570800	Weak transcription	HMEC	breast
4	chr2:48548600-48570600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:48552400-48570600	Weak transcription	Aorta	Aorta
6	chr2:48553400-48574400	Weak transcription	Lung	lung
7	chr2:48553800-48570800	Weak transcription	Thymus	Thymus
8	chr2:48554400-48570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:48555400-48570600	Weak transcription	NHLF	lung
10	chr2:48556800-48570600	Weak transcription	Fetal Thymus	thymus
11	chr2:48556800-48571600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:48557000-48573200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:48557000-48573400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:48557800-48570400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:48558400-48571400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:48558800-48571200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:48559000-48570600	Weak transcription	Left Ventricle	heart
18	chr2:48559000-48570600	Weak transcription	Spleen	Spleen
19	chr2:48559800-48570600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr2:48559800-48570600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:48559800-48573400	Weak transcription	Fetal Kidney	kidney
22	chr2:48559800-48573400	Weak transcription	Right Atrium	heart
23	chr2:48560600-48573600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:48561000-48571200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:48561600-48571400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:48561800-48571000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:48562000-48573400	Weak transcription	Psoas Muscle	Psoas
28	chr2:48562000-48573400	Weak transcription	K562	blood
29	chr2:48562200-48571000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:48564800-48574400	Weak transcription	Fetal Stomach	stomach
31	chr2:48565200-48570600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:48565200-48570800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:48565800-48570600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr2:48565800-48571800	Weak transcription	Fetal Intestine Small	intestine
35	chr2:48566000-48570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:48566200-48569200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr2:48566200-48570200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr2:48566200-48570600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:48566600-48569200	Enhancers	Primary T cells from cord blood	blood
40	chr2:48566600-48570200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr2:48566600-48573600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:48566800-48569800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:48566800-48570600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr2:48566800-48571000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:48567000-48570600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr2:48567200-48569000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:48567200-48571400	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr2:48567400-48570000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:48567400-48571000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:48567400-48571000	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links