Variant report

Variant	rs7959946
Chromosome Location	chr12:12381534-12381535
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs61733245	1.00[AMR][1000 genomes]
rs7137934	1.00[AMR][1000 genomes]
rs7297820	1.00[AMR][1000 genomes]
rs7297825	1.00[AMR][1000 genomes]
rs7305048	1.00[AMR][1000 genomes]
rs7311616	1.00[AMR][1000 genomes]
rs74064614	1.00[AMR][1000 genomes]
rs7973150	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12368200-12384200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:12370800-12392200	Weak transcription	Brain Substantia Nigra	brain
4	chr12:12374800-12383200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr12:12377400-12382400	Weak transcription	HSMM	muscle
6	chr12:12377800-12384200	Weak transcription	K562	blood
7	chr12:12377800-12407200	Weak transcription	NH-A	brain
8	chr12:12379200-12396800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:12379400-12382600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:12379400-12393600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:12379600-12384200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:12379600-12393600	Weak transcription	NHLF	lung
13	chr12:12379800-12382800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:12380000-12382400	Weak transcription	Fetal Kidney	kidney
15	chr12:12380000-12384200	Weak transcription	HepG2	liver
16	chr12:12380200-12384800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:12380200-12388800	Weak transcription	Fetal Intestine Small	intestine
18	chr12:12380400-12382600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:12380600-12382000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:12380800-12381800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr12:12380800-12381800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr12:12380800-12382000	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr12:12380800-12382000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr12:12380800-12382200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr12:12380800-12382600	Weak transcription	Brain Angular Gyrus	brain
26	chr12:12380800-12388400	Weak transcription	Fetal Stomach	stomach
27	chr12:12381000-12381600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr12:12381000-12381600	Enhancers	Left Ventricle	heart
29	chr12:12381000-12381800	Enhancers	Aorta	Aorta
30	chr12:12381000-12382000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr12:12381000-12383000	Enhancers	Brain Hippocampus Middle	brain
32	chr12:12381200-12381600	Enhancers	Lung	lung
33	chr12:12381200-12381600	Strong transcription	A549	lung
34	chr12:12381200-12382000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr12:12381200-12382000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:12381200-12382000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr12:12381200-12382000	Enhancers	Psoas Muscle	Psoas
38	chr12:12381200-12383000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:12381200-12387400	Enhancers	Liver	Liver
40	chr12:12381400-12381600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:12381400-12381600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:12381400-12381600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:12381400-12381600	Flanking Active TSS	Pancreas	Pancrea
44	chr12:12381400-12381800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:12381400-12381800	Enhancers	H9 Cell Line	embryonic stem cell
46	chr12:12381400-12381800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:12381400-12381800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:12381400-12381800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:12381400-12382000	Enhancers	Gastric	stomach
50	chr12:12381400-12382000	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links