Variant report

Variant	rs12294035
Chromosome Location	chr11:28139619-28139620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:28139467..28142149-chr11:28147133..28148730,2	K562	blood:
2	chr11:28138431..28141393-chr11:28141963..28144749,4	K562	blood:
3	chr11:28129230..28134284-chr11:28136584..28141196,8	K562	blood:

Variant related genes	Relation type
ENSG00000169519	Chromatin interaction
ENSG00000121621	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1032090	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1032091	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10767697	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10767705	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10767710	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10767712	0.83[ASN][1000 genomes]
rs10835259	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10835275	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10835280	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10835282	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10835286	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10835294	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10835296	0.86[EUR][1000 genomes]
rs10835298	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10835307	0.83[ASN][1000 genomes]
rs10835310	0.85[ASN][1000 genomes]
rs11030193	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11030197	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11030201	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11030203	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11030204	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11030223	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11030227	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11030228	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11030259	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11030262	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11030267	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12360577	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12361167	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12806548	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1384904	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1483861	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1564745	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1608871	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17244296	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2046372	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2128956	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2128958	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2140886	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2140887	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2354426	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4512801	0.82[ASN][1000 genomes]
rs4923522	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4923525	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6484352	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6484357	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6484361	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6484366	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7102481	0.82[ASN][1000 genomes]
rs7105075	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7107992	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7108140	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7117221	0.83[ASN][1000 genomes]
rs7121923	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7127104	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7128488	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7129953	0.86[EUR][1000 genomes]
rs7394692	0.81[ASN][1000 genomes]
rs7482650	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7924896	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7932126	0.85[ASN][1000 genomes]
rs7944852	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs960357	0.89[EUR][1000 genomes]
rs997555	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9988877	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832096	chr11:28020435-28155586	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv897150	chr11:28110210-28302792	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1040043	chr11:28118451-28170684	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv897151	chr11:28130191-28208464	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv897152	chr11:28130191-28218303	Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv38603	chr11:28138808-28143905	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:28132400-28156000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:28132600-28144600	Weak transcription	HSMMtube	muscle
3	chr11:28132600-28155800	Weak transcription	Esophagus	oesophagus
4	chr11:28132600-28157000	Weak transcription	Placenta	Placenta
5	chr11:28132600-28159000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:28132600-28160000	Weak transcription	Lung	lung
7	chr11:28132600-28160200	Weak transcription	Left Ventricle	heart
8	chr11:28132600-28161400	Weak transcription	Gastric	stomach
9	chr11:28132800-28140000	Weak transcription	Brain Germinal Matrix	brain
10	chr11:28132800-28142200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:28132800-28144600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:28132800-28151800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:28132800-28155400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:28132800-28155600	Weak transcription	Ovary	ovary
15	chr11:28132800-28156000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:28132800-28158000	Weak transcription	Psoas Muscle	Psoas
17	chr11:28132800-28158800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:28132800-28161000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:28132800-28161000	Weak transcription	Aorta	Aorta
20	chr11:28132800-28161000	Weak transcription	Brain Substantia Nigra	brain
21	chr11:28132800-28161200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:28132800-28161400	Weak transcription	Right Ventricle	heart
23	chr11:28133000-28140800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:28133000-28141000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:28133000-28144600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:28133000-28144600	Weak transcription	HMEC	breast
27	chr11:28133000-28144600	Weak transcription	NH-A	brain
28	chr11:28133000-28145600	Weak transcription	Brain Hippocampus Middle	brain
29	chr11:28133000-28154800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr11:28133000-28155000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:28133000-28159400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr11:28133000-28161600	Weak transcription	Colon Smooth Muscle	Colon
33	chr11:28133200-28144200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr11:28133200-28152800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr11:28133200-28155600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:28133400-28140200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr11:28133400-28149000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:28133400-28158000	Weak transcription	Brain Angular Gyrus	brain
39	chr11:28133600-28154600	Weak transcription	GM12878-XiMat	blood
40	chr11:28133600-28159000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr11:28133800-28144800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr11:28133800-28155200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr11:28133800-28156400	Weak transcription	Fetal Heart	heart
44	chr11:28133800-28157200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:28134200-28142200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr11:28134400-28156000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:28134400-28156800	Weak transcription	HepG2	liver
48	chr11:28135200-28139800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr11:28135800-28144400	Weak transcription	NHDF-Ad	bronchial
50	chr11:28135800-28147600	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links