Variant report

Variant	rs11169492
Chromosome Location	chr12:50959002-50959003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50947257..50949279-chr12:50958735..50961611,2	K562	blood:
2	chr12:50957129..50960260-chr12:50961650..50963740,3	K562	blood:
3	chr12:50957955..50959497-chr12:50959656..50962563,2	MCF-7	breast:
4	chr12:50958807..50961087-chr12:50974320..50976145,2	K562	blood:
5	chr12:50951293..50953796-chr12:50956997..50959240,2	MCF-7	breast:
6	chr12:50950342..50953589-chr12:50956085..50960023,3	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10747583	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783375	0.96[ASN][1000 genomes]
rs10876045	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876055	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876059	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876066	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876069	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10876074	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11169453	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169470	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169484	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169486	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169490	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169506	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11169523	0.90[AMR][1000 genomes]
rs11169524	0.92[AMR][1000 genomes]
rs12307178	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12372538	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12425362	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12427378	0.92[AMR][1000 genomes]
rs12582683	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12814717	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818741	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12825915	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1316442	0.86[AMR][1000 genomes]
rs1316607	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13378012	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1967576	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2090852	0.92[AMR][1000 genomes]
rs2139930	0.92[AMR][1000 genomes]
rs2243571	0.82[ASN][1000 genomes]
rs2280503	0.84[AMR][1000 genomes]
rs34553264	0.92[AMR][1000 genomes]
rs34682944	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3742062	0.88[AMR][1000 genomes]
rs3935138	0.99[ASN][1000 genomes]
rs3935870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4617661	0.93[ASN][1000 genomes]
rs4768847	0.92[ASN][1000 genomes]
rs61699126	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61926278	0.86[AMR][1000 genomes]
rs6580756	0.92[ASN][1000 genomes]
rs67092086	0.96[ASN][1000 genomes]
rs7133160	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7133687	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7137845	0.89[AMR][1000 genomes]
rs7298661	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7298665	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7302435	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7305375	0.85[ASN][1000 genomes]
rs7316864	0.99[ASN][1000 genomes]
rs7397999	0.99[ASN][1000 genomes]
rs7487429	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7965652	0.89[AMR][1000 genomes]
rs9788075	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[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	esv1820967	chr12:50856613-51002088	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11169492	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs11169492	ATF1	cis	Artery Tibial	GTEx
rs11169492	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50920800-50962400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:50927400-50961800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:50927800-50961800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:50932200-50961800	Weak transcription	Right Ventricle	heart
5	chr12:50936800-50962000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:50940000-50961400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:50940400-50961800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:50940800-50962000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:50941000-50961800	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:50941000-50962000	Weak transcription	Brain Germinal Matrix	brain
11	chr12:50941000-50963000	Weak transcription	HSMMtube	muscle
12	chr12:50944400-50962000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:50944600-50961800	Weak transcription	Small Intestine	intestine
14	chr12:50944800-50961800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:50945200-50965200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:50945400-50961800	Weak transcription	Esophagus	oesophagus
17	chr12:50947200-50961800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:50948400-50966000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:50948800-50961400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:50949400-50961800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:50949400-50962000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:50949400-50962000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr12:50949400-50973600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:50949800-50962000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:50949800-50962000	Weak transcription	Fetal Thymus	thymus
26	chr12:50950000-50961800	Weak transcription	Fetal Intestine Large	intestine
27	chr12:50951400-50961400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:50951600-50959200	Weak transcription	Dnd41	blood
29	chr12:50952000-50962000	Weak transcription	Fetal Intestine Small	intestine
30	chr12:50952000-50962000	Weak transcription	Fetal Stomach	stomach
31	chr12:50953400-50965600	Weak transcription	Primary B cells from cord blood	blood
32	chr12:50953800-50966000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:50954800-50959400	Enhancers	Liver	Liver
34	chr12:50955800-50960200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr12:50956200-50960000	Enhancers	HepG2	liver
36	chr12:50956200-50961000	Weak transcription	Stomach Mucosa	stomach
37	chr12:50956600-50961800	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:50957000-50959200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr12:50957200-50959200	Enhancers	Brain Substantia Nigra	brain
40	chr12:50957200-50965600	Weak transcription	Psoas Muscle	Psoas
41	chr12:50957400-50961800	Weak transcription	Left Ventricle	heart
42	chr12:50957600-50959200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:50957600-50959200	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr12:50957600-50959400	Enhancers	Brain Hippocampus Middle	brain
45	chr12:50957600-50959400	Enhancers	K562	blood
46	chr12:50957600-50959600	Enhancers	Brain Cingulate Gyrus	brain
47	chr12:50957600-50959800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr12:50957600-50959800	Weak transcription	Pancreas	Pancrea
49	chr12:50957600-50959800	Enhancers	NHEK	skin
50	chr12:50957600-50960400	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links