Variant report

Variant	rs836172
Chromosome Location	chr12:50490099-50490100
allele	C/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	POLR2A	chr12:50489559-50490272	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:50489688-50490103	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50471856..50474200-chr12:50488886..50490561,2	K562	blood:
2	chr12:50478513..50480166-chr12:50489047..50490966,2	K562	blood:
3	chr12:50488363..50491152-chr12:50496404..50499569,4	K562	blood:

Variant related genes	Relation type
SMARCD1	TF binding region
ENSG00000110881	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000167588	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1044370	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs10747570	0.81[ASN][1000 genomes]
rs11831413	0.80[ASN][1000 genomes]
rs12830386	0.80[ASN][1000 genomes]
rs1862043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1979702	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2178173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2272391	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs2358538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34573394	0.80[ASN][1000 genomes]
rs35549836	0.80[ASN][1000 genomes]
rs35998534	0.80[ASN][1000 genomes]
rs56709084	0.80[ASN][1000 genomes]
rs578470	0.80[EUR][1000 genomes]
rs646782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580729	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs706790	0.80[EUR][1000 genomes]
rs706791	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs706792	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs706793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7136570	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7279	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs7294548	0.80[ASN][1000 genomes]
rs7297421	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs7301649	0.80[ASN][1000 genomes]
rs7301740	0.84[ASN][1000 genomes]
rs7302981	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7308356	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7532	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs7967705	0.82[AMR][1000 genomes]
rs7972842	0.86[ASN][1000 genomes]
rs835592	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs836170	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836171	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836176	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836179	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs836180	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]
rs836181	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836188	0.80[EUR][1000 genomes]
rs844347	0.96[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs860698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs836172	LASS5	cis	multi-tissue	Pritchard
rs836172	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50480000-50494800	Strong transcription	Rectal Mucosa Donor 29	rectum
2	chr12:50480000-50496400	Weak transcription	Right Atrium	heart
3	chr12:50480200-50494800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:50480200-50494800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:50480200-50496200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr12:50480200-50496600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:50480200-50496600	Strong transcription	Thymus	Thymus
8	chr12:50480200-50496800	Strong transcription	Fetal Stomach	stomach
9	chr12:50480400-50493800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:50480400-50494400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr12:50480400-50494400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:50480400-50494600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:50480400-50494800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:50480400-50494800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr12:50480400-50494800	Strong transcription	Fetal Intestine Large	intestine
16	chr12:50480400-50494800	Strong transcription	Placenta	Placenta
17	chr12:50480400-50495600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr12:50480400-50495800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr12:50480400-50496000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:50480400-50496200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:50480400-50496200	Strong transcription	A549	lung
22	chr12:50480400-50496600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:50480400-50496600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:50480400-50496600	Strong transcription	Primary T cells from cord blood	blood
25	chr12:50480400-50496600	Strong transcription	Fetal Lung	lung
26	chr12:50480600-50491000	Strong transcription	Hela-S3	cervix
27	chr12:50480600-50492200	Strong transcription	Primary hematopoietic stem cells	blood
28	chr12:50480600-50493200	Strong transcription	Adipose Nuclei	Adipose
29	chr12:50480600-50493600	Strong transcription	HSMMtube	muscle
30	chr12:50480600-50494000	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr12:50480600-50494600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:50480600-50494600	Strong transcription	Left Ventricle	heart
33	chr12:50480600-50494800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr12:50480600-50494800	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:50480600-50495000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr12:50480600-50495000	Strong transcription	Spleen	Spleen
37	chr12:50480600-50495400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:50480600-50495800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:50480800-50494800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr12:50480800-50495000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:50480800-50496400	Strong transcription	Fetal Thymus	thymus
42	chr12:50481000-50494400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:50481000-50496000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:50481400-50494000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:50481600-50496800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:50482000-50494600	Strong transcription	Lung	lung
47	chr12:50482000-50495400	Strong transcription	Fetal Muscle Leg	muscle
48	chr12:50482000-50496600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:50482400-50491800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr12:50482400-50493000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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