Variant report

Variant	rs836180
Chromosome Location	chr12:50503269-50503270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr12:50502880-50507261	SK-N-SH	brain:	n/a	n/a
2	RFX5	chr12:50503133-50506733	IMR90	lung:	n/a	n/a
3	HCFC1	chr12:50502851-50506900	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50475972..50484033-chr12:50500850..50507517,14	K562	blood:
2	chr12:50491501..50494072-chr12:50502085..50505008,3	K562	blood:
3	chr12:50478595..50483647-chr12:50502911..50507517,7	K562	blood:
4	chr12:50503233..50504882-chr12:50521389..50523983,2	K562	blood:
5	chr12:50467168..50469530-chr12:50502079..50503763,2	MCF-7	breast:
6	chr12:50499334..50507442-chr12:50559441..50562987,11	K562	blood:

No data

Variant related genes	Relation type
COX14	TF binding region
ENSG00000272368	TF binding region
ENSG00000110881	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000066117	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1044370	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs10747570	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169294	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11831413	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12815871	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12824125	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12830386	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862043	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2178173	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2358538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34573394	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35549836	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35998534	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56709084	0.90[ASN][1000 genomes]
rs646782	0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6580729	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66768395	0.84[ASN][1000 genomes]
rs706791	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs706792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs706793	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7136570	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7279	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7294548	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7297421	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7301649	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7301740	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7302981	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7308356	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967705	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7967844	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7972842	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs835592	0.80[TSI][hapmap]
rs836170	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs836171	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs836172	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs836173	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs836174	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs836176	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs836177	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs836179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836181	0.80[ASN][1000 genomes]
rs844347	0.84[GIH][hapmap]
rs860698	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs836180	SNORA2A	cis	parietal	SCAN
rs836180	KRT84	cis	cerebellum	SCAN
rs836180	MCRS1	cis	parietal	SCAN
rs836180	TMEM106C	cis	cerebellum	SCAN
rs836180	LASS5	cis	parietal	SCAN
rs836180	LASS5	cis	multi-tissue	Pritchard
rs836180	LASS5	cis	cerebellum	SCAN
rs836180	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:102 , 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	chr12:50494000-50503400	Weak transcription	Aorta	Aorta
8	chr12:50494000-50503600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:50494000-50504200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:50494000-50504400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:50494000-50505200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:50494800-50503400	Weak transcription	NHDF-Ad	bronchial
13	chr12:50494800-50505000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:50495000-50504000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:50495000-50504800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:50495600-50504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:50495600-50504200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:50495800-50505200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:50496000-50503400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:50496000-50504200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr12:50496200-50503800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:50496200-50504200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:50496200-50504800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:50496400-50504600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:50496600-50503800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:50496600-50503800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:50496600-50504400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr12:50496600-50504600	Weak transcription	Primary T cells from cord blood	blood
29	chr12:50496800-50503400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:50496800-50504800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:50498000-50503400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:50498000-50503800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:50498200-50503400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:50498200-50503600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:50498400-50503800	Weak transcription	HSMM	muscle
36	chr12:50498400-50503800	Weak transcription	NHEK	skin
37	chr12:50498600-50504000	Weak transcription	HSMMtube	muscle
38	chr12:50498800-50503600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:50499000-50503800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr12:50499200-50504000	Weak transcription	Gastric	stomach
41	chr12:50499400-50503600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:50499400-50504600	Weak transcription	Colon Smooth Muscle	Colon
43	chr12:50499600-50503400	Weak transcription	Brain Anterior Caudate	brain
44	chr12:50499600-50503400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:50499600-50503400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:50499600-50504400	Weak transcription	Fetal Lung	lung
47	chr12:50499800-50504800	Weak transcription	Fetal Brain Female	brain
48	chr12:50500000-50503400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:50500000-50503600	Weak transcription	Brain Angular Gyrus	brain
50	chr12:50500200-50503400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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