Variant report

Variant	rs12496956
Chromosome Location	chr3:43647659-43647660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:43645888..43649296-chr3:43657154..43659992,5	K562	blood:
2	chr3:43644364..43653636-chr3:43657183..43664965,16	K562	blood:
3	chr3:43645317..43647771-chr3:43731333..43734292,2	K562	blood:
4	chr3:43643230..43645081-chr3:43645455..43648410,2	K562	blood:

Variant related genes	Relation type
ENSG00000160746	Chromatin interaction
ENSG00000011198	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1564614	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17075787	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1972449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2888332	0.97[AMR][1000 genomes]
rs3772164	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3772168	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428738	chr3:43491435-43651168	Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv834673	chr3:43622985-43799876	Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43574800-43662400	Weak transcription	Right Ventricle	heart
2	chr3:43589000-43648400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:43614600-43653800	Weak transcription	HepG2	liver
4	chr3:43618600-43649600	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:43618600-43654400	Weak transcription	Colonic Mucosa	Colon
6	chr3:43618600-43662400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:43622200-43648400	Weak transcription	HMEC	breast
8	chr3:43624000-43657600	Weak transcription	Psoas Muscle	Psoas
9	chr3:43625800-43662600	Weak transcription	Primary T cells from cord blood	blood
10	chr3:43626200-43652400	Weak transcription	Osteobl	bone
11	chr3:43633200-43654800	Weak transcription	Small Intestine	intestine
12	chr3:43633200-43662400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:43633400-43648800	Weak transcription	Placenta	Placenta
14	chr3:43633400-43653800	Weak transcription	Gastric	stomach
15	chr3:43633400-43657800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:43633400-43662000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:43633400-43662600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:43633400-43662600	Weak transcription	Pancreas	Pancrea
19	chr3:43634000-43648800	Weak transcription	Lung	lung
20	chr3:43634000-43652600	Weak transcription	Fetal Intestine Large	intestine
21	chr3:43634000-43652800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:43634000-43658000	Weak transcription	Left Ventricle	heart
23	chr3:43634000-43662400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:43634000-43662600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:43634000-43662600	Weak transcription	Ovary	ovary
26	chr3:43634200-43658000	Weak transcription	Fetal Stomach	stomach
27	chr3:43634400-43662000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:43634600-43662400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:43634800-43650800	Weak transcription	Fetal Lung	lung
30	chr3:43635200-43659800	Weak transcription	Aorta	Aorta
31	chr3:43635200-43662600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:43637000-43659400	Weak transcription	Brain Substantia Nigra	brain
33	chr3:43637800-43660000	Weak transcription	Brain Anterior Caudate	brain
34	chr3:43639400-43662400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:43639800-43662200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:43640000-43647800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:43640000-43650000	Weak transcription	NH-A	brain
38	chr3:43640000-43653800	Weak transcription	Liver	Liver
39	chr3:43641200-43652400	Weak transcription	Fetal Intestine Small	intestine
40	chr3:43642000-43662400	Weak transcription	Brain Germinal Matrix	brain
41	chr3:43642800-43647800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:43643600-43657600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:43644200-43653800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:43645400-43662400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:43645400-43662400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:43645600-43648200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:43645600-43657600	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:43646200-43649200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:43646200-43649800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:43646200-43659600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links