Variant report

Variant	rs836178
Chromosome Location	chr12:50498139-50498140
allele	G/T
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	POLR2A	chr12:50497610-50498316	HepG2	liver:	n/a	n/a
2	MAX	chr12:50497480-50498270	HepG2	liver:	n/a	chr12:50497727-50497737 chr12:50498037-50498047
3	POLR2A	chr12:50497472-50499365	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:50495195-50498322	HepG2	liver:	n/a	n/a
5	MAZ	chr12:50497545-50498158	HepG2	liver:	n/a	chr12:50497727-50497737 chr12:50498037-50498047
6	POLR2A	chr12:50497534-50498157	K562	blood:	n/a	n/a
7	MXI1	chr12:50497239-50498163	SK-N-SH	brain:	n/a	chr12:50497746-50497755
8	MAX	chr12:50497481-50498205	ECC-1	luminal epithelium:	n/a	chr12:50497727-50497737 chr12:50498037-50498047

No.	Distal block	Cell Line	Cell type
1	chr12:50496593..50501221-chr12:50560690..50564425,5	MCF-7	breast:
2	chr12:50488363..50491152-chr12:50496404..50499569,4	K562	blood:
3	chr12:50497524..50499290-chr12:51157685..51160627,2	MCF-7	breast:
4	chr12:50477688..50480373-chr12:50497434..50499573,3	K562	blood:
5	chr12:50496807..50498530-chr12:50498901..50501416,2	K562	blood:
6	chr12:50477670..50481382-chr12:50495555..50500836,7	K562	blood:

Variant related genes	Relation type
GPD1	TF binding region
ENSG00000123268	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000167588	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10875995	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs10875996	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169270	0.92[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs11169282	0.85[GIH][hapmap]
rs1554844	0.85[GIH][hapmap]
rs17124432	0.85[GIH][hapmap]
rs3741562	0.85[GIH][hapmap]
rs376184	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]
rs404751	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs439171	0.91[JPT][hapmap]
rs450423	0.83[JPT][hapmap]
rs484951	0.92[JPT][hapmap]
rs4898546	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs590460	0.92[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs613066	0.92[JPT][hapmap]
rs685012	0.90[CHB][hapmap];0.83[JPT][hapmap];0.90[TSI][hapmap]
rs706789	0.83[CHD][hapmap];0.92[JPT][hapmap]
rs706794	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7294618	0.85[GIH][hapmap]
rs7307230	0.85[GIH][hapmap]
rs7961065	0.85[GIH][hapmap]
rs7961112	0.85[GIH][hapmap]
rs7968119	0.81[ASN][1000 genomes]
rs835593	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs836175	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs836184	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs844359	0.90[CHB][hapmap];1.00[JPT][hapmap]

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
rs836178	LASS5	cis	cerebellum	SCAN
rs836178	ATF1	cis	parietal	SCAN
rs836178	SLC38A1	cis	parietal	SCAN
rs836178	SNORA2A	cis	parietal	SCAN
rs836178	AQP6	cis	parietal	SCAN
rs836178	CERS5	cis	Nerve Tibial	GTEx
rs836178	LASS5	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50490600-50504200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:50492200-50504400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:50492400-50504800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:50492600-50504200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:50492600-50504600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:50493600-50504400	Weak transcription	Small Intestine	intestine
7	chr12:50494000-50499000	Weak transcription	Fetal Kidney	kidney
8	chr12:50494000-50503200	Weak transcription	GM12878-XiMat	blood
9	chr12:50494000-50503400	Weak transcription	Aorta	Aorta
10	chr12:50494000-50503600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:50494000-50504200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:50494000-50504400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:50494000-50505200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:50494600-50500400	Enhancers	Fetal Brain Male	brain
15	chr12:50494800-50503400	Weak transcription	NHDF-Ad	bronchial
16	chr12:50494800-50505000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:50495000-50504000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr12:50495000-50504800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr12:50495600-50504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:50495600-50504200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:50495800-50503000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:50495800-50505200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:50496000-50503400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:50496000-50504200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr12:50496200-50498400	Enhancers	Ovary	ovary
26	chr12:50496200-50500000	Enhancers	Brain Angular Gyrus	brain
27	chr12:50496200-50500800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr12:50496200-50503000	Weak transcription	A549	lung
29	chr12:50496200-50503800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:50496200-50504200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:50496200-50504800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:50496400-50498200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr12:50496400-50499200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:50496400-50504600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:50496600-50498600	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr12:50496600-50499000	Enhancers	H1 Cell Line	embryonic stem cell
37	chr12:50496600-50503000	Weak transcription	Thymus	Thymus
38	chr12:50496600-50503800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:50496600-50503800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:50496600-50504400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:50496600-50504600	Weak transcription	Primary T cells from cord blood	blood
42	chr12:50496800-50498600	Enhancers	Fetal Heart	heart
43	chr12:50496800-50499000	Weak transcription	Primary B cells from cord blood	blood
44	chr12:50496800-50499200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:50496800-50503400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:50496800-50504800	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr12:50497000-50498200	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr12:50497000-50499600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:50497200-50498400	Enhancers	Fetal Thymus	thymus
50	chr12:50497200-50498800	Enhancers	Right Atrium	heart

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