Variant report

Variant	rs3136344
Chromosome Location	chr2:48030022-48030023
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:48029803-48030172	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:48029867-48030903	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:48029860-48031487	GM12892	blood:	n/a	n/a
4	POLR2A	chr2:48029639-48030080	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:48023000-48032172	A549	lung:	n/a	n/a
6	POLR2A	chr2:48022886-48032233	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:48029703-48030056	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr2:48029835-48031000	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr2:48029511-48032220	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr2:48029884-48032154	K562	blood:	n/a	n/a
11	POLR2A	chr2:48029846-48031429	GM12892	blood:	n/a	n/a
12	POLR2A	chr2:48029942-48030076	GM12891	blood:	n/a	n/a
13	POLR2A	chr2:48029998-48030784	K562	blood:	n/a	n/a
14	POLR2A	chr2:48029843-48030102	K562	blood:	n/a	n/a
15	POLR2A	chr2:48029320-48032222	GM12892	blood:	n/a	n/a
16	POLR2A	chr2:48022295-48040595	K562	blood:	n/a	n/a
17	POLR2A	chr2:48029950-48030412	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:48030015-48030213	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:48029795-48030098	GM12892	blood:	n/a	n/a
20	POLR2A	chr2:48029813-48030208	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:48029798-48030209	PFSK-1	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:48028902..48031846-chr2:48031868..48034895,3	K562	blood:
2	chr2:48009689..48012474-chr2:48029068..48031018,2	K562	blood:
3	chr2:48016706..48019633-chr2:48029423..48031526,2	K562	blood:
4	chr2:48008730..48016091-chr2:48023378..48031018,13	K562	blood:
5	chr2:48029284..48031152-chr2:48035129..48037209,2	MCF-7	breast:

No data

Variant related genes	Relation type
RPL36AP15	TF binding region
ENSG00000138081	Chromatin interaction
ENSG00000116062	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17395820	0.82[AMR][1000 genomes]
rs1800937	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3136229	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136230	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3136243	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3136277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3136290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3136300	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3136326	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3136357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41540312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription 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	36 gene(s)	inside rSNPs	diseases
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48012600-48065000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:48016200-48050400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:48016800-48030200	Strong transcription	Fetal Muscle Leg	muscle
4	chr2:48017000-48036200	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr2:48017000-48049400	Strong transcription	Fetal Intestine Large	intestine
6	chr2:48017200-48053200	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:48017400-48032200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:48017400-48049600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr2:48017800-48037800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:48018000-48030200	Strong transcription	Brain Germinal Matrix	brain
11	chr2:48018000-48030400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:48018200-48030200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:48018200-48030200	Strong transcription	Fetal Brain Female	brain
14	chr2:48018200-48030600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:48018400-48030200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:48018600-48030200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:48019600-48030600	Strong transcription	Liver	Liver
18	chr2:48020800-48030200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:48020800-48030400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:48021200-48030400	Strong transcription	Fetal Lung	lung
21	chr2:48021200-48036200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:48021200-48036400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:48021200-48051600	Strong transcription	Placenta	Placenta
24	chr2:48021400-48030200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:48021400-48030200	Strong transcription	Fetal Kidney	kidney
26	chr2:48021400-48030200	Strong transcription	Thymus	Thymus
27	chr2:48021400-48030400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:48021400-48030400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr2:48021400-48030600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:48021400-48032600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:48021400-48037200	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr2:48021400-48067600	Strong transcription	Dnd41	blood
33	chr2:48021600-48030200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr2:48021600-48030400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:48021600-48030600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:48021600-48030600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:48021600-48030600	Strong transcription	NH-A	brain
38	chr2:48021600-48037400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:48021600-48037800	Strong transcription	HepG2	liver
40	chr2:48021600-48067000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:48021800-48030200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:48021800-48030400	Strong transcription	Primary T cells from cord blood	blood
43	chr2:48021800-48035200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:48021800-48037400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:48021800-48039800	Strong transcription	Brain Anterior Caudate	brain
46	chr2:48022000-48036200	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr2:48022000-48041400	Strong transcription	HSMM	muscle
48	chr2:48022200-48030600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr2:48022200-48037600	Strong transcription	Osteobl	bone
50	chr2:48022200-48050200	Strong transcription	Rectal Mucosa Donor 29	rectum

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