Variant report

Variant	rs35671537
Chromosome Location	chr12:9817395-9817396
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	CEBPB	chr12:9817218-9817490	K562	blood:	n/a	chr12:9817384-9817395
2	CEBPB	chr12:9817238-9817544	HepG2	liver:	n/a	chr12:9817384-9817395
3	CEBPB	chr12:9817264-9817544	A549	lung:	n/a	chr12:9817384-9817395
4	CEBPB	chr12:9817288-9817558	IMR90	lung:	n/a	chr12:9817384-9817395

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9810242..9813132-chr12:9813704..9817912,3	MCF-7	breast:
2	chr12:9799537..9802341-chr12:9814175..9817797,3	K562	blood:

Variant related genes	Relation type
CLEC2D	TF binding region
ENSG00000256442	Chromatin interaction
ENSG00000256594	Chromatin interaction
ENSG00000257027	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10466762	1.00[ASN][1000 genomes]
rs10772005	1.00[ASN][1000 genomes]
rs10772006	1.00[ASN][1000 genomes]
rs10844236	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844267	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10844327	1.00[ASN][1000 genomes]
rs10844350	1.00[ASN][1000 genomes]
rs10844351	1.00[ASN][1000 genomes]
rs10844352	1.00[ASN][1000 genomes]
rs10844353	1.00[ASN][1000 genomes]
rs10844359	1.00[ASN][1000 genomes]
rs10844369	0.89[ASN][1000 genomes]
rs11052207	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052209	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052234	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052235	1.00[ASN][1000 genomes]
rs11052245	1.00[ASN][1000 genomes]
rs11052254	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052282	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11608817	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12310789	1.00[ASN][1000 genomes]
rs12317691	0.83[AFR][1000 genomes]
rs12366653	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366792	1.00[ASN][1000 genomes]
rs12809846	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12820641	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12830419	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12831287	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560008	1.00[ASN][1000 genomes]
rs16913477	1.00[ASN][1000 genomes]
rs1863871	1.00[ASN][1000 genomes]
rs2114869	1.00[ASN][1000 genomes]
rs2162657	1.00[ASN][1000 genomes]
rs34323946	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34833649	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34981673	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35015427	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35098654	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35181877	0.89[ASN][1000 genomes]
rs35280686	1.00[ASN][1000 genomes]
rs35561167	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35642909	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35884213	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55873283	1.00[ASN][1000 genomes]
rs61916061	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6488065	0.89[ASN][1000 genomes]
rs7132037	1.00[ASN][1000 genomes]
rs7136821	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299738	1.00[ASN][1000 genomes]
rs7302110	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302746	1.00[ASN][1000 genomes]
rs7303246	0.89[ASN][1000 genomes]
rs7304321	1.00[ASN][1000 genomes]
rs7304464	1.00[ASN][1000 genomes]
rs7305937	1.00[ASN][1000 genomes]
rs7309800	1.00[ASN][1000 genomes]
rs7310405	1.00[ASN][1000 genomes]
rs7310516	1.00[ASN][1000 genomes]
rs7310568	1.00[ASN][1000 genomes]
rs7310790	1.00[ASN][1000 genomes]
rs7311421	1.00[ASN][1000 genomes]
rs7311574	1.00[ASN][1000 genomes]
rs7311945	1.00[ASN][1000 genomes]
rs7959406	1.00[ASN][1000 genomes]
rs7959726	1.00[ASN][1000 genomes]
rs7961262	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961416	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962321	1.00[ASN][1000 genomes]
rs7967102	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7973603	1.00[ASN][1000 genomes]
rs7974871	1.00[ASN][1000 genomes]
rs7978187	1.00[ASN][1000 genomes]
rs958340	1.00[ASN][1000 genomes]
rs9919786	1.00[ASN][1000 genomes]
rs9919787	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs35671537	CLEC2D	cis	Thyroid	GTEx
rs35671537	LOC374443	cis	brain	BrainEAC
rs35671537	CLEC2D	cis	Esophagus Muscularis	GTEx
rs35671537	LOC374443	Cis_1M	lymphoblastoid	RTeQTL
rs35671537	RP11-705C15.3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9803000-9819800	Weak transcription	Fetal Brain Female	brain
3	chr12:9803000-9820200	Weak transcription	Brain Substantia Nigra	brain
4	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
5	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
6	chr12:9804400-9820400	Weak transcription	HUVEC	blood vessel
7	chr12:9804600-9820000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:9804600-9820000	Weak transcription	HMEC	breast
9	chr12:9804600-9820200	Weak transcription	NHEK	skin
10	chr12:9805600-9819400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:9805800-9818200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:9806000-9818000	Strong transcription	Fetal Muscle Leg	muscle
13	chr12:9806200-9818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:9806200-9818200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:9806200-9819000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr12:9806200-9821600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:9806600-9818000	Strong transcription	Placenta	Placenta
18	chr12:9806600-9818600	Strong transcription	Adipose Nuclei	Adipose
19	chr12:9806600-9818600	Strong transcription	Fetal Lung	lung
20	chr12:9807000-9818000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:9807000-9818200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr12:9807000-9826000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:9808000-9817800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:9808000-9820000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:9808200-9818200	Genic enhancers	Primary T cells from cord blood	blood
27	chr12:9808400-9818200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:9808600-9819200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
29	chr12:9808800-9819200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr12:9810600-9817800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:9811200-9818000	Strong transcription	Left Ventricle	heart
32	chr12:9812000-9818200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr12:9812000-9820400	Weak transcription	NHLF	lung
34	chr12:9812200-9817600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:9812800-9825800	Weak transcription	Right Ventricle	heart
36	chr12:9813000-9825800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:9813000-9826200	Weak transcription	Brain Anterior Caudate	brain
38	chr12:9813000-9826200	Weak transcription	Gastric	stomach
39	chr12:9813400-9818000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:9813600-9818600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:9813800-9826000	Weak transcription	NHDF-Ad	bronchial
42	chr12:9814000-9818000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:9814000-9818800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:9814600-9818200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr12:9814600-9818200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:9814600-9819200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr12:9814600-9819600	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr12:9814800-9818200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr12:9814800-9818600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:9814800-9820000	Weak transcription	A549	lung

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