Variant report

Variant	rs16860748
Chromosome Location	chr3:112980515-112980516
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11917869	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs11919091	1.00[AMR][1000 genomes]
rs11920233	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs11922003	1.00[AMR][1000 genomes]
rs11925633	1.00[AMR][1000 genomes]
rs11926656	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs11929188	1.00[AMR][1000 genomes]
rs16845110	1.00[AMR][1000 genomes]
rs16860700	1.00[AMR][1000 genomes]
rs16860716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860752	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860782	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860800	1.00[AMR][1000 genomes]
rs16860854	1.00[AMR][1000 genomes]
rs16860875	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs16861019	1.00[AMR][1000 genomes]
rs4082653	1.00[AMR][1000 genomes]
rs7430385	1.00[AMR][1000 genomes]
rs7651839	1.00[AMR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112961600-112983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:112969600-112981000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
5	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
6	chr3:112970200-112981000	Weak transcription	Gastric	stomach
7	chr3:112970200-112981000	Weak transcription	Pancreas	Pancrea
8	chr3:112971800-112986400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:112972000-112980600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:112972400-112986400	Weak transcription	Fetal Intestine Small	intestine
11	chr3:112973400-112981800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:112973400-112982600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:112973400-112987600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:112973600-112982000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:112973600-112983600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:112973600-112993000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
18	chr3:112973800-112981200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:112973800-112981800	Weak transcription	Psoas Muscle	Psoas
20	chr3:112973800-112983400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:112974200-112981000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:112974200-112981400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:112974200-112981800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:112974200-112994600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:112974600-112981400	Weak transcription	Brain Anterior Caudate	brain
26	chr3:112974600-112982200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:112974800-112981800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:112974800-112983200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:112975400-112981000	Weak transcription	Brain Substantia Nigra	brain
30	chr3:112975600-112981000	Weak transcription	HSMM	muscle
31	chr3:112976400-112980600	Weak transcription	HSMMtube	muscle
32	chr3:112976400-112981600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:112976400-112988600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:112976600-112981200	Enhancers	Colon Smooth Muscle	Colon
35	chr3:112976800-112982000	Enhancers	Rectal Smooth Muscle	rectum
36	chr3:112977600-112981800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:112977800-112982200	Enhancers	Adipose Nuclei	Adipose
38	chr3:112978600-112983800	Weak transcription	Brain Angular Gyrus	brain
39	chr3:112978600-112991400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:112978800-112980800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:112978800-112984400	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr3:112979200-112981200	Enhancers	Fetal Muscle Leg	muscle
43	chr3:112979400-112981400	Enhancers	Aorta	Aorta
44	chr3:112979400-112984800	Genic enhancers	Fetal Stomach	stomach
45	chr3:112979600-112981800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:112979600-112985600	Enhancers	Fetal Brain Female	brain
47	chr3:112979800-112980800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:112979800-112981000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:112980000-112980800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:112980000-112981000	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links