Variant report

Variant	rs11169030
Chromosome Location	chr12:49855209-49855210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49759570..49762166-chr12:49852805..49855688,2	MCF-7	breast:
2	chr12:49759519..49761735-chr12:49853453..49856491,3	K562	blood:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10467104	1.00[AFR][1000 genomes]
rs11168994	1.00[AFR][1000 genomes]
rs11169036	1.00[AFR][1000 genomes]
rs11169072	1.00[AFR][1000 genomes]
rs11169077	1.00[AFR][1000 genomes]
rs11169096	1.00[AFR][1000 genomes]
rs11169119	1.00[AFR][1000 genomes]
rs12297088	1.00[AFR][1000 genomes]
rs12299386	1.00[AFR][1000 genomes]
rs12300053	1.00[AFR][1000 genomes]
rs12305870	1.00[AFR][1000 genomes]
rs12309765	1.00[AFR][1000 genomes]
rs12310439	1.00[AFR][1000 genomes]
rs12313145	1.00[AFR][1000 genomes]
rs12322175	1.00[AFR][1000 genomes]
rs12322207	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
2	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49798400-49856000	Weak transcription	Primary T cells from cord blood	blood
2	chr12:49823000-49856000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:49823000-49915800	Weak transcription	Primary B cells from cord blood	blood
4	chr12:49823200-49856000	Weak transcription	NHEK	skin
5	chr12:49823200-49856400	Weak transcription	HSMM	muscle
6	chr12:49823400-49856000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:49823400-49857400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:49823400-49876000	Weak transcription	Osteobl	bone
9	chr12:49828000-49863400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:49837600-49856000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:49839200-49876000	Weak transcription	Fetal Thymus	thymus
12	chr12:49840200-49900600	Weak transcription	Pancreas	Pancrea
13	chr12:49840600-49856000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:49840600-49875800	Weak transcription	Hela-S3	cervix
15	chr12:49840800-49856000	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:49841800-49855800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:49843400-49856000	Weak transcription	Fetal Stomach	stomach
18	chr12:49845600-49856000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:49845800-49856800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:49846000-49879800	Weak transcription	Fetal Lung	lung
21	chr12:49846400-49878400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr12:49846800-49856000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:49847000-49858200	Weak transcription	Fetal Brain Female	brain
24	chr12:49848000-49856000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:49848200-49856000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:49848400-49856000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:49849400-49856000	Weak transcription	Ovary	ovary
28	chr12:49849400-49856000	Weak transcription	Psoas Muscle	Psoas
29	chr12:49849400-49875800	Weak transcription	HepG2	liver
30	chr12:49849600-49856000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:49849600-49869800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:49850000-49856000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:49850000-49856000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:49850000-49856000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:49850000-49856000	Weak transcription	Gastric	stomach
36	chr12:49850000-49856000	Weak transcription	Left Ventricle	heart
37	chr12:49850000-49856000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:49850000-49856200	Weak transcription	Aorta	Aorta
39	chr12:49850000-49858800	Weak transcription	Fetal Kidney	kidney
40	chr12:49850200-49856000	Weak transcription	Right Ventricle	heart
41	chr12:49850400-49856000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:49850400-49876000	Weak transcription	Fetal Intestine Large	intestine
43	chr12:49850400-49876000	Weak transcription	Small Intestine	intestine
44	chr12:49850400-49878800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:49850400-49911000	Weak transcription	K562	blood
46	chr12:49850600-49876200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:49851000-49856000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:49852400-49856000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:49852600-49856000	Weak transcription	Fetal Intestine Small	intestine
50	chr12:49853200-49876000	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links