Variant report

Variant	rs1772405
Chromosome Location	chr1:159010001-159010002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1057027	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1057028	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1101991	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs1101993	0.83[CEU][hapmap]
rs1101995	0.82[CEU][hapmap]
rs1101998	0.81[CEU][hapmap]
rs11265132	0.84[EUR][1000 genomes]
rs11265133	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs12090965	0.84[EUR][1000 genomes]
rs12093523	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs12094545	0.84[EUR][1000 genomes]
rs12094692	0.84[EUR][1000 genomes]
rs12094741	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs12094786	0.84[EUR][1000 genomes]
rs12124059	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12144575	0.84[EUR][1000 genomes]
rs12239136	0.84[EUR][1000 genomes]
rs12240111	0.84[EUR][1000 genomes]
rs1417804	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1614182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1616024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[ASN][1000 genomes]
rs1633256	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1633262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1633265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1633266	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1633267	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1772407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1772408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1772414	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1772415	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2106094	0.84[EUR][1000 genomes]
rs2106095	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs2157694	0.84[EUR][1000 genomes]
rs2157695	0.84[EUR][1000 genomes]
rs2518553	0.90[EUR][1000 genomes]
rs2570916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2840312	0.84[EUR][1000 genomes]
rs2852699	0.93[ASN][1000 genomes]
rs56235865	0.84[EUR][1000 genomes]
rs56374780	0.84[EUR][1000 genomes]
rs60958912	0.84[EUR][1000 genomes]
rs66831955	0.84[EUR][1000 genomes]
rs67772786	0.84[EUR][1000 genomes]
rs67843408	0.84[EUR][1000 genomes]
rs73021886	0.84[EUR][1000 genomes]
rs7513121	0.86[YRI][hapmap]
rs7535630	0.84[EUR][1000 genomes]
rs7538035	0.84[EUR][1000 genomes]
rs7545770	0.84[EUR][1000 genomes]
rs855865	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs855866	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs856051	0.83[EUR][1000 genomes]
rs856052	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs856053	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs856054	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs856055	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs856056	0.90[EUR][1000 genomes]
rs856057	0.90[EUR][1000 genomes]
rs856058	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs861318	1.00[CEU][hapmap];0.90[EUR][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	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1772405	AIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
3	chr1:158984200-159024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:158984800-159027400	Weak transcription	Psoas Muscle	Psoas
5	chr1:158985400-159023800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:158986000-159016200	Weak transcription	Stomach Mucosa	stomach
7	chr1:158988200-159016600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:158988600-159024000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:158993000-159023200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:158997600-159017000	Strong transcription	Primary B cells from cord blood	blood
11	chr1:158998400-159024000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr1:158998600-159014600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:158998600-159015600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:158998800-159014000	Strong transcription	Primary T cells from cord blood	blood
15	chr1:158998800-159033800	Weak transcription	Fetal Brain Female	brain
16	chr1:158999000-159014400	Strong transcription	Fetal Intestine Large	intestine
17	chr1:158999000-159022800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:158999200-159023800	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:158999400-159013000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:158999600-159013000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:159000000-159012800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:159000000-159012800	Strong transcription	NHEK	skin
23	chr1:159000000-159026200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:159000200-159011800	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr1:159000200-159013200	Strong transcription	Primary hematopoietic stem cells	blood
26	chr1:159000200-159013400	Strong transcription	Thymus	Thymus
27	chr1:159000400-159014000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:159000400-159024200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:159000600-159014200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:159000600-159020200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:159000600-159023800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:159000800-159010800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:159001000-159016000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:159001000-159016600	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:159001000-159027400	Weak transcription	Right Ventricle	heart
36	chr1:159001200-159014400	Strong transcription	Ovary	ovary
37	chr1:159001200-159017200	Strong transcription	HUVEC	blood vessel
38	chr1:159001400-159010400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:159001400-159010800	Weak transcription	Aorta	Aorta
40	chr1:159001400-159014200	Strong transcription	Adipose Nuclei	Adipose
41	chr1:159001400-159020200	Weak transcription	Brain Anterior Caudate	brain
42	chr1:159001400-159020200	Weak transcription	Gastric	stomach
43	chr1:159001400-159024200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:159001400-159036200	Weak transcription	Small Intestine	intestine
45	chr1:159001600-159028400	Strong transcription	Fetal Thymus	thymus
46	chr1:159002200-159010200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:159002400-159010200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:159003000-159011600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:159003000-159022000	Weak transcription	Fetal Brain Male	brain
50	chr1:159003400-159021400	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links