Variant report

Variant	rs2143890
Chromosome Location	chr6:88193626-88193627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:88193616-88193942	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUND	chr6:88193574-88194742	HCT-116	colon:	n/a	n/a
3	JUND	chr6:88193625-88193972	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr6:88193589-88194158	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:88193428-88194018	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:88193572-88193940	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUND	chr6:88193610-88194102	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:88193470-88194103	HCT-116	colon:	n/a	n/a
9	FOSL1	chr6:88193459-88194848	HCT-116	colon:	n/a	n/a
10	TEAD4	chr6:88193591-88194056	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:88193620-88193702	MCF-7	breast:	n/a	n/a
12	SP1	chr6:88193381-88194873	HCT-116	colon:	n/a	n/a
13	JUND	chr6:88193387-88194803	HCT-116	colon:	n/a	n/a
14	BACH1	chr6:88193622-88194007	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr6:88193478-88194042	HCT-116	colon:	n/a	n/a
16	POLR2A	chr6:88193512-88193875	H1-hESC	embryonic stem cell:	n/a	n/a
17	CBX3	chr6:88193569-88194755	HCT-116	colon:	n/a	chr6:88194716-88194727
18	SP1	chr6:88193497-88194784	HCT-116	colon:	n/a	n/a
19	FOSL1	chr6:88193561-88194705	HCT-116	colon:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88181541..88186084-chr6:88193253..88197004,5	MCF-7	breast:
2	chr6:88187817..88189806-chr6:88192099..88194936,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-444P	TF binding region
ENSG00000164414	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11962148	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12524203	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12524205	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13195393	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16879893	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2092649	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2246057	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2268995	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2268996	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300898	0.92[ASN][1000 genomes]
rs2300899	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300900	0.92[ASN][1000 genomes]
rs2300904	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2300907	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300908	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3778671	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818057	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58785365	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6903332	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6927171	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6928057	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6931177	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7383567	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7761943	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444509	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450708	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450709	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450711	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450716	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450717	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450719	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450721	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2143890	SLC35A1	cis	multi-tissue	Pritchard
rs2143890	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88183600-88212800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:88183600-88226000	Weak transcription	Gastric	stomach
3	chr6:88183800-88193800	Weak transcription	Colonic Mucosa	Colon
4	chr6:88183800-88197000	Weak transcription	NH-A	brain
5	chr6:88183800-88204200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:88183800-88210800	Weak transcription	Adipose Nuclei	Adipose
7	chr6:88183800-88211000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:88183800-88211000	Weak transcription	Brain Anterior Caudate	brain
9	chr6:88183800-88211000	Weak transcription	Thymus	Thymus
10	chr6:88183800-88211800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:88183800-88212000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:88183800-88212600	Weak transcription	Psoas Muscle	Psoas
13	chr6:88183800-88216400	Weak transcription	K562	blood
14	chr6:88183800-88219800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:88183800-88221000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:88183800-88221000	Weak transcription	Fetal Kidney	kidney
17	chr6:88183800-88225400	Weak transcription	Aorta	Aorta
18	chr6:88183800-88227400	Weak transcription	Right Ventricle	heart
19	chr6:88184000-88200800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:88184000-88202400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:88184000-88210800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr6:88184000-88211000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr6:88184000-88211000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:88184000-88218600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:88184000-88218600	Weak transcription	Brain Angular Gyrus	brain
26	chr6:88184000-88218800	Weak transcription	Brain Germinal Matrix	brain
27	chr6:88184000-88219800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:88184000-88221000	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:88184000-88224200	Weak transcription	Hela-S3	cervix
30	chr6:88184200-88211000	Weak transcription	NHDF-Ad	bronchial
31	chr6:88184200-88214800	Weak transcription	Fetal Brain Male	brain
32	chr6:88184400-88195400	Weak transcription	HepG2	liver
33	chr6:88184400-88204600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:88184400-88211200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:88184400-88211800	Weak transcription	Brain Substantia Nigra	brain
36	chr6:88185000-88196400	Weak transcription	HUVEC	blood vessel
37	chr6:88185800-88211400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:88186000-88211400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:88187800-88210800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:88188400-88202800	Weak transcription	Fetal Brain Female	brain
41	chr6:88188400-88208200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:88188400-88211000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr6:88188600-88221600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:88188800-88205400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr6:88188800-88210800	Weak transcription	Left Ventricle	heart
46	chr6:88189200-88211200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:88190200-88202600	Weak transcription	Osteobl	bone
48	chr6:88190600-88193800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr6:88191200-88194000	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr6:88191200-88227400	Weak transcription	Spleen	Spleen

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