Variant report

Variant	rs790156
Chromosome Location	chr5:127491565-127491566
allele	C/T
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	chr5:127491560-127491710	AG04450	lung:	n/a	n/a
2	CTCF	chr5:127491540-127491690	AG09319	gingival:	n/a	n/a
3	PBX3	chr5:127491270-127491644	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr5:127491263-127491754	SK-N-SH	brain:	n/a	n/a
5	EP300	chr5:127491271-127491614	SK-N-SH_RA	brain:	n/a	chr5:127491337-127491347
6	CTCF	chr5:127491534-127491734	GM12878	blood:	n/a	n/a
7	PBX3	chr5:127491187-127491721	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr5:127491560-127491710	HPAF	blood vessel:	n/a	n/a
9	RAD21	chr5:127491521-127491772	SK-N-SH_RA	brain:	n/a	n/a
10	RAD21	chr5:127491535-127491795	SK-N-SH_RA	brain:	n/a	n/a
11	CTCF	chr5:127491557-127491750	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127477463..127479784-chr5:127489454..127492343,3	K562	blood:
2	chr5:127489489..127491992-chr5:127501991..127503642,2	K562	blood:

Variant related genes	Relation type
SLC12A2	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10039525	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10060390	0.87[YRI][hapmap]
rs10061367	0.95[YRI][hapmap]
rs10063647	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs10067555	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap]
rs10478798	0.87[YRI][hapmap]
rs10478803	0.95[YRI][hapmap]
rs13357268	0.87[YRI][hapmap]
rs1432614	0.95[YRI][hapmap]
rs1432615	0.86[YRI][hapmap]
rs1864922	0.85[LWK][hapmap];0.95[YRI][hapmap]
rs1864923	0.95[YRI][hapmap]
rs2001524	0.89[ASN][1000 genomes]
rs251215	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs251217	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs251388	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3792866	0.82[LWK][hapmap];0.95[YRI][hapmap]
rs3805606	0.85[LWK][hapmap];0.95[YRI][hapmap]
rs3816006	0.95[YRI][hapmap]
rs4835941	0.87[YRI][hapmap]
rs4836361	0.86[YRI][hapmap]
rs6862701	0.86[YRI][hapmap]
rs7713860	0.83[YRI][hapmap]
rs7718286	0.95[YRI][hapmap]
rs790153	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs806100	0.86[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs809841	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs883074	0.85[LWK][hapmap];0.95[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830482	chr5:127475398-127665377	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs790156	CTC-228N24.3	cis	Skin Sun Exposed Lower leg	GTEx
rs790156	LOC644869	cis	multi-tissue	Pritchard
rs790156	SLC12A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127423600-127494000	Weak transcription	K562	blood
2	chr5:127441200-127536800	Weak transcription	Colonic Mucosa	Colon
3	chr5:127442400-127525000	Weak transcription	Right Ventricle	heart
4	chr5:127445400-127491800	Weak transcription	Psoas Muscle	Psoas
5	chr5:127447000-127525000	Weak transcription	Fetal Brain Male	brain
6	chr5:127453600-127493800	Weak transcription	Liver	Liver
7	chr5:127453600-127525400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:127454400-127493800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:127457600-127534400	Weak transcription	Pancreas	Pancrea
10	chr5:127460800-127525200	Weak transcription	Spleen	Spleen
11	chr5:127463200-127533000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:127464800-127497600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:127465400-127532200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr5:127467200-127500600	Weak transcription	Esophagus	oesophagus
15	chr5:127467600-127525000	Weak transcription	Thymus	Thymus
16	chr5:127467800-127508000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:127468000-127536800	Weak transcription	Fetal Brain Female	brain
18	chr5:127468800-127493800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:127469200-127524200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr5:127469800-127504200	Weak transcription	Fetal Heart	heart
21	chr5:127471200-127515200	Weak transcription	Brain Germinal Matrix	brain
22	chr5:127471800-127499800	Weak transcription	NHLF	lung
23	chr5:127472400-127498800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr5:127473600-127521800	Weak transcription	Fetal Kidney	kidney
25	chr5:127474400-127491800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr5:127474400-127493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr5:127478000-127514400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:127478400-127500200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:127478400-127524600	Weak transcription	Small Intestine	intestine
30	chr5:127478600-127531600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr5:127478800-127497600	Weak transcription	NH-A	brain
32	chr5:127479200-127532200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:127480600-127501600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:127480600-127532400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:127480600-127534400	Weak transcription	Gastric	stomach
36	chr5:127482600-127499000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:127483000-127499200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:127483000-127500200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:127483200-127495600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr5:127483800-127491800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr5:127484200-127494000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:127484200-127499000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr5:127484400-127493000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr5:127484400-127495400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:127485000-127536800	Weak transcription	Colon Smooth Muscle	Colon
46	chr5:127485800-127492000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr5:127485800-127497800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:127486000-127491800	Weak transcription	A549	lung
49	chr5:127486800-127491600	Strong transcription	Adipose Nuclei	Adipose
50	chr5:127486800-127500000	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links