Variant report

Variant	rs4696289
Chromosome Location	chr4:152621237-152621238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152609052..152613001-chr4:152620763..152623852,3	MCF-7	breast:
2	chr4:152620191..152622280-chr4:152625003..152626689,2	K562	blood:

Variant related genes	Relation type
ENSG00000059691	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10001603	0.80[EUR][1000 genomes]
rs10007653	0.80[EUR][1000 genomes]
rs10022023	0.82[EUR][1000 genomes]
rs1107797	0.83[CEU][hapmap];0.94[GIH][hapmap];0.91[MKK][hapmap]
rs11723395	0.81[EUR][1000 genomes]
rs11723438	0.81[EUR][1000 genomes]
rs11726892	0.81[EUR][1000 genomes]
rs11736116	0.81[EUR][1000 genomes]
rs11931934	0.81[EUR][1000 genomes]
rs11932059	0.81[EUR][1000 genomes]
rs12645029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12649199	0.84[EUR][1000 genomes]
rs12650655	0.81[EUR][1000 genomes]
rs12651635	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17275598	0.82[EUR][1000 genomes]
rs17275724	0.94[GIH][hapmap]
rs17360371	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17360385	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1822346	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1822347	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2407069	0.81[EUR][1000 genomes]
rs4696098	1.00[CEU][hapmap]
rs4696099	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs4696101	0.80[EUR][1000 genomes]
rs4696102	0.81[EUR][1000 genomes]
rs4696266	0.91[CEU][hapmap]
rs4696268	0.88[CEU][hapmap]
rs4696272	0.81[EUR][1000 genomes]
rs4696275	0.81[EUR][1000 genomes]
rs4696276	0.81[EUR][1000 genomes]
rs4696278	0.81[EUR][1000 genomes]
rs4696279	0.82[EUR][1000 genomes]
rs4696280	0.81[EUR][1000 genomes]
rs4696281	0.80[EUR][1000 genomes]
rs4696288	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696290	0.83[EUR][1000 genomes]
rs55808836	0.80[EUR][1000 genomes]
rs62327269	0.81[EUR][1000 genomes]
rs62327270	0.81[EUR][1000 genomes]
rs62327271	0.81[EUR][1000 genomes]
rs62327274	0.80[AFR][1000 genomes]
rs62327275	0.80[AFR][1000 genomes]
rs62327277	0.81[EUR][1000 genomes]
rs62327278	0.81[EUR][1000 genomes]
rs62327349	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62327350	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6811676	0.81[EUR][1000 genomes]
rs6816471	1.00[CEU][hapmap]
rs6833814	0.80[AFR][1000 genomes]
rs6836249	0.87[CEU][hapmap]
rs718800	0.81[EUR][1000 genomes]
rs718801	0.81[EUR][1000 genomes]
rs7674244	1.00[CEU][hapmap]
rs7678080	0.81[EUR][1000 genomes]
rs7683134	1.00[CEU][hapmap]
rs7685697	0.81[EUR][1000 genomes]
rs7689266	0.82[EUR][1000 genomes]
rs7692700	0.81[EUR][1000 genomes]
rs7695412	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs7695866	1.00[CEU][hapmap]
rs875667	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs875668	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4551	chr4:152582617-152627367	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv508322	chr4:152617079-152678951	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4696289	FAM160A1	cis	cerebellum	SCAN
rs4696289	PET112L	cis	parietal	SCAN
rs4696289	PET112L	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152563800-152625200	Weak transcription	Hela-S3	cervix
2	chr4:152585600-152628600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:152585800-152640400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:152591200-152646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:152592600-152636400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:152596200-152624000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:152596400-152627800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:152596400-152628600	Weak transcription	Colonic Mucosa	Colon
9	chr4:152596400-152640600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:152598400-152648200	Weak transcription	HMEC	breast
11	chr4:152599000-152637200	Weak transcription	GM12878-XiMat	blood
12	chr4:152600600-152626200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:152603000-152623200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:152605400-152628600	Weak transcription	Aorta	Aorta
15	chr4:152608800-152622200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:152609000-152622800	Weak transcription	A549	lung
17	chr4:152609200-152622200	Weak transcription	Placenta	Placenta
18	chr4:152609200-152640200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:152609600-152621600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:152609600-152622000	Weak transcription	Thymus	Thymus
21	chr4:152609600-152628800	Weak transcription	HepG2	liver
22	chr4:152609600-152640400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:152609800-152622400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:152609800-152646200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:152610800-152621800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:152611000-152623200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:152611800-152640000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:152612000-152622200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr4:152612000-152651000	Weak transcription	K562	blood
30	chr4:152612200-152628800	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:152612200-152632600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:152612400-152631800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:152612400-152642600	Weak transcription	NHLF	lung
34	chr4:152612600-152622200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:152612600-152630000	Weak transcription	NH-A	brain
36	chr4:152612800-152628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:152613000-152621600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:152613000-152622800	Weak transcription	NHEK	skin
39	chr4:152613000-152627000	Weak transcription	Brain Germinal Matrix	brain
40	chr4:152613000-152629000	Weak transcription	Osteobl	bone
41	chr4:152613400-152621400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:152613400-152621800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:152613400-152622800	Weak transcription	Fetal Kidney	kidney
44	chr4:152614000-152626200	Weak transcription	Fetal Thymus	thymus
45	chr4:152614200-152622400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:152614200-152622400	Weak transcription	Spleen	Spleen
47	chr4:152614400-152622200	Weak transcription	Right Ventricle	heart
48	chr4:152614400-152640200	Weak transcription	Gastric	stomach
49	chr4:152614600-152621800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:152614600-152621800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links