Variant report

Variant	rs3993375
Chromosome Location	chr12:83358419-83358420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1023967	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1025556	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10778923	0.91[GIH][hapmap];1.00[JPT][hapmap]
rs10862533	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12821905	0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs1796156	0.87[CHD][hapmap]
rs7296753	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7298790	1.00[JPT][hapmap]
rs7300355	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7308937	1.00[ASN][1000 genomes]
rs7956157	0.81[GIH][hapmap]
rs7960659	1.00[JPT][hapmap]
rs892539	0.87[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv832472	chr12:83248283-83419753	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	nsv559557	chr12:83334204-83453620	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
6	nsv469495	chr12:83339933-83374779	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	nsv559558	chr12:83339933-83374779	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3993375	SLC6A15	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83347000-83367200	Weak transcription	Gastric	stomach
2	chr12:83347000-83379600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:83349400-83374600	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:83356200-83379400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:83356400-83381600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:83356600-83359200	Enhancers	Brain Hippocampus Middle	brain
7	chr12:83356600-83381400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:83357600-83358600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr12:83357800-83358600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:83357800-83358600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr12:83357800-83358600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr12:83357800-83358600	Enhancers	Fetal Muscle Leg	muscle
13	chr12:83357800-83358800	Enhancers	Brain Germinal Matrix	brain
14	chr12:83357800-83359000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:83357800-83363200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr12:83357800-83389600	Weak transcription	Fetal Intestine Large	intestine
17	chr12:83358000-83358600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr12:83358000-83358600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:83358000-83358600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr12:83358000-83358600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:83358000-83359200	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr12:83358000-83389600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:83358200-83358600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:83358200-83358600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:83358200-83366200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:83358200-83368400	Weak transcription	Fetal Stomach	stomach
27	chr12:83358400-83358600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:83358400-83358600	Enhancers	Pancreas	Pancrea
29	chr12:83358400-83358600	Enhancers	Stomach Smooth Muscle	stomach
30	chr12:83358400-83359200	Weak transcription	Fetal Lung	lung
31	chr12:83358400-83361600	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr12:83358400-83363000	Weak transcription	Fetal Brain Male	brain
33	chr12:83358400-83366400	Weak transcription	Brain Substantia Nigra	brain
34	chr12:83358400-83397600	Weak transcription	Brain Anterior Caudate	brain
35	chr12:83358400-83409200	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links