Variant report

Variant	rs2238145
Chromosome Location	chr12:48113772-48113773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:48113740-48113890	GM12872	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48097267..48105309-chr12:48111877..48120917,8	MCF-7	breast:
2	chr12:48099768..48101524-chr12:48112369..48115075,3	K562	blood:
3	chr12:48113473..48116472-chr12:48126075..48128753,2	MCF-7	breast:
4	chr12:48113590..48115252-chr12:48167578..48169438,2	K562	blood:
5	chr12:48112866..48115065-chr12:48225593..48227392,2	K562	blood:
6	chr12:48113366..48116147-chr12:48117513..48120473,4	MCF-7	breast:
7	chr12:48111612..48114264-chr12:48135856..48138068,2	K562	blood:
8	chr12:48113489..48115457-chr12:48167332..48169028,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC48A1-1	chr12:48113685-48113899	ENSG00000257433

No data

Variant related genes	Relation type
ENDOU	TF binding region
ENSG00000257433	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000111405	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1233062	0.93[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072116	0.92[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3829317	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757282	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7977774	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs886431	1.00[CEU][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs929270	1.00[YRI][hapmap];0.96[AFR][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	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48102800-48125000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:48111000-48113800	Enhancers	Esophagus	oesophagus
3	chr12:48111400-48116000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:48111400-48124000	Weak transcription	Gastric	stomach
5	chr12:48111600-48115800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:48111800-48114600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:48111800-48114800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:48111800-48114800	Weak transcription	Thymus	Thymus
9	chr12:48111800-48115200	Weak transcription	Primary T cells from cord blood	blood
10	chr12:48111800-48116000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:48111800-48117000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:48112000-48114600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:48112000-48115000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr12:48112000-48115000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:48112000-48115200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:48112000-48115200	Weak transcription	HSMM	muscle
17	chr12:48112000-48115200	Weak transcription	HSMMtube	muscle
18	chr12:48112000-48115400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:48112000-48115400	Weak transcription	Osteobl	bone
20	chr12:48112000-48116000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:48112000-48116400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:48112000-48116400	Weak transcription	Psoas Muscle	Psoas
23	chr12:48112000-48117000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:48112000-48118200	Weak transcription	Fetal Intestine Large	intestine
25	chr12:48112000-48118400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:48112000-48120000	Weak transcription	Fetal Lung	lung
27	chr12:48112000-48120000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:48112000-48122800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:48112000-48123000	Weak transcription	Pancreas	Pancrea
30	chr12:48112000-48126800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:48112200-48114400	Weak transcription	Fetal Intestine Small	intestine
32	chr12:48112200-48114600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr12:48112200-48114800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:48112200-48114800	Weak transcription	NHDF-Ad	bronchial
35	chr12:48112200-48115000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:48112200-48115000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:48112200-48115200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:48112200-48115200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:48112200-48115200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr12:48112200-48116400	Weak transcription	Aorta	Aorta
41	chr12:48112200-48116400	Weak transcription	Brain Angular Gyrus	brain
42	chr12:48112200-48116400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:48112200-48117200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:48112200-48118600	Weak transcription	Stomach Mucosa	stomach
45	chr12:48112200-48119000	Weak transcription	Colonic Mucosa	Colon
46	chr12:48112200-48119200	Weak transcription	GM12878-XiMat	blood
47	chr12:48112200-48125400	Weak transcription	Fetal Thymus	thymus
48	chr12:48112200-48127000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:48112400-48113800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr12:48112400-48114800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links