Variant report

Variant	rs11169506
Chromosome Location	chr12:51011256-51011257
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50951137..50952780-chr12:51008933..51011689,2	MCF-7	breast:
2	chr12:51007874..51011257-chr12:51018084..51021009,3	K562	blood:
3	chr12:50943053..50945273-chr12:51008692..51011511,2	K562	blood:
4	chr12:50898604..50900466-chr12:51010594..51012574,2	MCF-7	breast:
5	chr12:50973979..50976902-chr12:51009398..51011703,2	MCF-7	breast:
6	chr12:51010106..51013321-chr12:51014428..51017771,4	K562	blood:
7	chr12:51005135..51007601-chr12:51009064..51012183,3	K562	blood:
8	chr12:51010956..51013399-chr12:51030994..51033191,2	MCF-7	breast:
9	chr12:51009757..51011293-chr12:51019509..51021830,2	K562	blood:
10	chr12:50898246..50903498-chr12:51010215..51015015,10	MCF-7	breast:
11	chr12:50924997..50928021-chr12:51009408..51011641,3	MCF-7	breast:
12	chr12:51010138..51012030-chr17:57922744..57924361,2	MCF-7	breast:
13	chr12:51007721..51011700-chr12:51012673..51015464,4	MCF-7	breast:
14	chr12:50925303..50926862-chr12:51010690..51012401,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000066084	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1047912	0.92[CEU][hapmap]
rs10747583	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10783387	0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap]
rs10876045	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10876055	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10876059	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10876066	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10876069	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10876074	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876084	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11169453	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11169484	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11169486	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11169490	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11169492	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11169520	0.95[CEU][hapmap]
rs11169523	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169567	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs1129406	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs12307178	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12372538	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12372718	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap]
rs12425362	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12427378	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12582683	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12814717	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12818741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825915	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1316442	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1316607	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13378012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1967576	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2090852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2139930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2264734	0.91[ASN][1000 genomes]
rs2280503	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2684908	0.88[CHB][hapmap]
rs2700478	0.97[ASN][1000 genomes]
rs34553264	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3742062	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3935138	0.89[CHB][hapmap]
rs3935870	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4388959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4768903	0.92[CEU][hapmap]
rs4986838	0.94[CHB][hapmap]
rs61699126	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61926278	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580761	0.88[CHB][hapmap]
rs7133160	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7133687	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7133974	0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap]
rs7137845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7298661	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7298665	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7302435	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7305375	0.80[ASN][1000 genomes]
rs7306677	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7309964	0.96[CEU][hapmap]
rs7487429	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7955736	0.96[CEU][hapmap]
rs7965652	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs876080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9788075	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	esv1822840	chr12:50973897-51015509	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11169506	DIP2B	cis	Lymphoblastoid	GTEx
rs11169506	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs11169506	KIAA1463	cis	multi-tissue	Pritchard
rs11169506	DIP2B	cis	multi-tissue	Pritchard
rs11169506	ATF1	cis	Artery Tibial	GTEx
rs11169506	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50974000-51011800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:50979200-51013800	Weak transcription	Fetal Stomach	stomach
3	chr12:50991600-51014000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:50992400-51015200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:50993000-51013800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr12:50993000-51013800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:50993600-51013400	Weak transcription	GM12878-XiMat	blood
8	chr12:50994400-51012400	Weak transcription	Primary T cells from cord blood	blood
9	chr12:50994600-51018600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:50997600-51013000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:50997600-51014200	Weak transcription	Spleen	Spleen
12	chr12:50998000-51012000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:50998600-51013000	Weak transcription	Gastric	stomach
14	chr12:51001000-51012000	Weak transcription	Fetal Intestine Large	intestine
15	chr12:51001400-51012800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:51003600-51013200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr12:51003600-51015400	Enhancers	Brain Hippocampus Middle	brain
18	chr12:51005000-51013600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:51005600-51013200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:51005600-51013800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:51005800-51013800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:51006000-51014000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:51006000-51014200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:51006200-51012800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:51006200-51012800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:51006200-51014000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:51006600-51016000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:51007000-51012200	Weak transcription	Fetal Intestine Small	intestine
29	chr12:51007000-51013200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:51007000-51017600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr12:51007200-51013600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:51007400-51014000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr12:51007600-51012000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr12:51007600-51012800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:51007600-51013200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:51007600-51013200	Weak transcription	Aorta	Aorta
37	chr12:51007600-51014200	Weak transcription	Primary B cells from cord blood	blood
38	chr12:51008200-51014600	Weak transcription	Fetal Kidney	kidney
39	chr12:51008400-51012000	Weak transcription	Right Atrium	heart
40	chr12:51008400-51012800	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:51008400-51012800	Weak transcription	Pancreas	Pancrea
42	chr12:51008400-51013000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:51008400-51013200	Weak transcription	Right Ventricle	heart
44	chr12:51008400-51013800	Weak transcription	Adipose Nuclei	Adipose
45	chr12:51008600-51012000	Weak transcription	Esophagus	oesophagus
46	chr12:51008600-51013000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:51008600-51013200	Weak transcription	Left Ventricle	heart
48	chr12:51008600-51013200	Weak transcription	NHLF	lung
49	chr12:51008600-51013800	Weak transcription	Psoas Muscle	Psoas
50	chr12:51008600-51014200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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