Variant report

Variant	rs376184
Chromosome Location	chr12:50474040-50474041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr12:50473351-50474121	ECC-1	luminal epithelium:	n/a	chr12:50473629-50473637
2	REST	chr12:50473339-50474125	ECC-1	luminal epithelium:	n/a	chr12:50473629-50473637

No.	Distal block	Cell Line	Cell type
1	chr12:50450867..50453197-chr12:50472058..50474772,2	MCF-7	breast:
2	chr12:50466696..50474949-chr12:50474970..50481457,17	MCF-7	breast:
3	chr12:50472028..50474859-chr12:50477717..50480636,3	MCF-7	breast:
4	chr12:50471491..50474468-chr12:50505629..50507284,2	K562	blood:
5	chr12:50465539..50467962-chr12:50472151..50474107,2	K562	blood:
6	chr12:50471856..50474200-chr12:50488886..50490561,2	K562	blood:

Variant related genes	Relation type
ASIC1	TF binding region
SMARCD1	TF binding region
ENSG00000066117	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10875995	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs10875996	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11169270	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs11169282	0.84[GIH][hapmap]
rs1554844	0.84[GIH][hapmap]
rs17124432	0.84[GIH][hapmap]
rs3741562	0.84[GIH][hapmap]
rs386469	0.87[ASN][1000 genomes]
rs393848	0.91[ASN][1000 genomes]
rs404751	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs439171	0.80[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs450423	0.80[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs484951	0.80[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs4898546	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56990521	0.88[EUR][1000 genomes]
rs590460	0.96[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs613066	0.80[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs627869	0.89[ASN][1000 genomes]
rs627887	0.89[ASN][1000 genomes]
rs653576	0.85[ASN][1000 genomes]
rs685012	0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs706789	0.80[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs706794	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294618	0.84[GIH][hapmap]
rs7307230	0.84[GIH][hapmap]
rs73299515	0.81[EUR][1000 genomes]
rs73299518	0.82[EUR][1000 genomes]
rs7956491	0.81[EUR][1000 genomes]
rs7961065	0.84[GIH][hapmap]
rs7961112	0.84[GIH][hapmap]
rs835591	0.85[ASN][1000 genomes]
rs835593	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs835594	0.92[ASN][1000 genomes]
rs836175	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs836178	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs836184	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs836185	0.86[ASN][1000 genomes]
rs836186	0.90[ASN][1000 genomes]
rs844359	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs860699	0.85[ASN][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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs376184	SNORA2A	cis	parietal	SCAN
rs376184	ATF1	cis	parietal	SCAN
rs376184	AQP6	cis	parietal	SCAN
rs376184	SLC38A1	cis	parietal	SCAN
rs376184	CERS5	cis	Nerve Tibial	GTEx
rs376184	LASS5	cis	parietal	SCAN
rs376184	LASS5	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50458200-50478200	Weak transcription	Thymus	Thymus
2	chr12:50464400-50478200	Weak transcription	Fetal Heart	heart
3	chr12:50464400-50478200	Weak transcription	Right Atrium	heart
4	chr12:50464800-50474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:50464800-50478200	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:50464800-50478200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:50464800-50478200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:50464800-50478400	Weak transcription	Primary T cells from cord blood	blood
9	chr12:50466800-50474800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:50469400-50474400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:50469400-50474800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:50469400-50474800	Weak transcription	Right Ventricle	heart
13	chr12:50469400-50478200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:50469400-50478200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:50469400-50478200	Weak transcription	Fetal Brain Male	brain
16	chr12:50469600-50474400	Weak transcription	K562	blood
17	chr12:50469600-50474600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:50469600-50474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:50469600-50477000	Strong transcription	Fetal Brain Female	brain
20	chr12:50469600-50477600	Weak transcription	HMEC	breast
21	chr12:50469600-50478200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:50469600-50478200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:50469600-50478200	Weak transcription	Brain Angular Gyrus	brain
24	chr12:50469600-50478200	Weak transcription	Brain Anterior Caudate	brain
25	chr12:50469600-50478200	Weak transcription	Fetal Lung	lung
26	chr12:50469600-50478200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:50469800-50476000	Weak transcription	Colonic Mucosa	Colon
28	chr12:50469800-50478200	Weak transcription	Gastric	stomach
29	chr12:50470000-50478200	Weak transcription	Liver	Liver
30	chr12:50470600-50474600	Strong transcription	Fetal Stomach	stomach
31	chr12:50471200-50476200	Strong transcription	Brain Germinal Matrix	brain
32	chr12:50471400-50477600	Weak transcription	GM12878-XiMat	blood
33	chr12:50471600-50474800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:50471800-50474800	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr12:50472200-50475600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:50472600-50478000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:50472600-50478200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:50473400-50475800	Enhancers	HepG2	liver
39	chr12:50473400-50478200	Enhancers	Fetal Intestine Large	intestine
40	chr12:50473600-50474800	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:50473600-50475800	Enhancers	Fetal Intestine Small	intestine
42	chr12:50473800-50474800	Weak transcription	Lung	lung
43	chr12:50474000-50478200	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links