Variant report

Variant	rs7136570
Chromosome Location	chr12:50529936-50529937
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	CTCF	chr12:50529840-50529990	AG09309	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50526517..50529253-chr12:50529891..50532313,2	MCF-7	breast:
2	chr12:50529645..50533801-chr12:50534954..50538460,5	MCF-7	breast:
3	chr12:50529914..50531795-chr12:50537950..50540041,2	K562	blood:
4	chr12:50477499..50479020-chr12:50528748..50530881,2	MCF-7	breast:

Variant related genes	Relation type
CERS5	TF binding region
ENSG00000066117	Chromatin interaction
ENSG00000139624	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1044370	0.90[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs10747570	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169294	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11831413	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12426261	0.83[EUR][1000 genomes]
rs12815871	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12824125	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12830386	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1862043	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2178173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2358538	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs34573394	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35549836	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35998534	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4459386	0.89[ASW][hapmap];0.89[YRI][hapmap]
rs4883481	0.83[EUR][1000 genomes]
rs4883482	0.81[EUR][1000 genomes]
rs56709084	0.94[ASN][1000 genomes]
rs646782	1.00[CHB][hapmap]
rs6580729	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66768395	0.88[ASN][1000 genomes]
rs706791	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs706792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs706793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7279	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];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294548	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297421	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];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7301649	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7301740	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7302981	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308356	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7532	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7957659	0.89[ASW][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap]
rs7967705	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7967844	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7972842	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs836171	0.80[ASN][1000 genomes]
rs836172	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs836177	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs836179	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836180	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]
rs844347	0.84[GIH][hapmap]
rs860698	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7136570	KRT84	cis	cerebellum	SCAN
rs7136570	LASS5	cis	cerebellum	SCAN
rs7136570	CERS5	cis	Nerve Tibial	GTEx
rs7136570	LASS5	cis	multi-tissue	Pritchard
rs7136570	SNORA2A	cis	parietal	SCAN
rs7136570	DIP2B	cis	cerebellum	SCAN
rs7136570	LASS5	cis	parietal	SCAN
rs7136570	MCRS1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50507000-50537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
3	chr12:50507200-50532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:50511200-50538200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:50511400-50538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:50512600-50538200	Strong transcription	Primary B cells from cord blood	blood
7	chr12:50516000-50532400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr12:50516600-50536200	Strong transcription	Fetal Intestine Large	intestine
9	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:50518000-50532400	Strong transcription	HSMM	muscle
11	chr12:50519200-50538200	Strong transcription	Fetal Muscle Leg	muscle
12	chr12:50519400-50538400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:50519600-50532600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:50519600-50537800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:50519600-50538200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr12:50520200-50537800	Strong transcription	Primary T cells from cord blood	blood
17	chr12:50520200-50539000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:50520400-50530600	Strong transcription	Fetal Stomach	stomach
19	chr12:50520400-50538000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:50520600-50533800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:50520600-50537400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:50520600-50537800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:50520600-50537800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:50520600-50538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:50520600-50538200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:50520600-50538200	Strong transcription	Fetal Thymus	thymus
27	chr12:50520600-50538400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:50520600-50538600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:50520600-50538600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:50520800-50532400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:50520800-50532800	Strong transcription	Dnd41	blood
32	chr12:50520800-50537800	Strong transcription	Fetal Lung	lung
33	chr12:50520800-50538200	Strong transcription	Thymus	Thymus
34	chr12:50521000-50532600	Strong transcription	Placenta	Placenta
35	chr12:50521200-50538400	Strong transcription	HSMMtube	muscle
36	chr12:50521400-50537200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:50521600-50538400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr12:50522400-50530000	Strong transcription	K562	blood
39	chr12:50522600-50533000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:50522800-50532400	Strong transcription	NHEK	skin
41	chr12:50522800-50533200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr12:50522800-50538200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:50522800-50538400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:50522800-50538600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:50523000-50530800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr12:50523000-50537200	Strong transcription	Fetal Brain Female	brain
47	chr12:50523400-50538600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:50523600-50530000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:50523600-50530000	Strong transcription	Esophagus	oesophagus
50	chr12:50523600-50537800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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