Variant report

Variant	rs11869625
Chromosome Location	chr17:46177362-46177363
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46175023..46180196-chr17:46181333..46189268,23	MCF-7	breast:
2	chr17:46177274..46179922-chr17:46706362..46708559,2	K562	blood:
3	chr17:46125418..46126971-chr17:46177352..46179960,2	K562	blood:
4	chr17:46124025..46127922-chr17:46176725..46180326,7	MCF-7	breast:
5	chr17:46122869..46127022-chr17:46176971..46180616,11	MCF-7	breast:
6	chr17:46123351..46126971-chr17:46177351..46182209,7	K562	blood:
7	chr17:46174648..46181471-chr17:46183317..46187457,20	MCF-7	breast:
8	chr17:46177349..46182213-chr17:46183318..46186399,5	K562	blood:
9	chr17:46177349..46180853-chr17:46182060..46186447,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000082641	Chromatin interaction
ENSG00000242207	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000263412	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1010228	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10853094	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079806	0.83[AMR][1000 genomes]
rs11079807	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11079808	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11079809	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11651097	0.83[AMR][1000 genomes]
rs11655407	0.83[AMR][1000 genomes]
rs12450620	0.83[AMR][1000 genomes]
rs12600980	0.81[ASN][1000 genomes]
rs12602948	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12936731	0.83[AMR][1000 genomes]
rs12941295	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12943543	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12949879	0.83[AMR][1000 genomes]
rs12950213	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12950402	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12952163	0.83[AMR][1000 genomes]
rs1860866	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2051821	0.80[AMR][1000 genomes]
rs2109984	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2285863	0.80[AMR][1000 genomes]
rs35361214	0.85[AMR][1000 genomes]
rs35688835	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3744346	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3744347	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4794441	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4794442	0.94[ASN][1000 genomes]
rs4794443	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4794448	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4794449	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4794450	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4794451	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4794453	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58203448	0.83[AMR][1000 genomes]
rs58595405	0.83[AMR][1000 genomes]
rs58624511	0.83[AMR][1000 genomes]
rs62064953	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6504024	0.86[AMR][1000 genomes]
rs6504025	0.86[AMR][1000 genomes]
rs6504031	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6504032	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6847	0.83[AMR][1000 genomes]
rs7209585	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7209730	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7212202	0.83[AMR][1000 genomes]
rs7213339	0.80[AMR][1000 genomes]
rs7217496	0.83[AMR][1000 genomes]
rs7218700	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7220520	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7221441	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7222136	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7224014	0.83[AMR][1000 genomes]
rs8065670	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8065993	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8066049	0.80[ASN][1000 genomes]
rs8066391	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs8069889	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8075500	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8076380	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8077860	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8078125	0.83[AMR][1000 genomes]
rs8080662	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs875065	0.83[AMR][1000 genomes]
rs9747001	0.83[AMR][1000 genomes]
rs978263	0.81[ASN][1000 genomes]
rs9807087	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9890691	0.81[ASN][1000 genomes]
rs9899275	0.83[AMR][1000 genomes]
rs9899461	0.83[AMR][1000 genomes]
rs9910516	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11869625	SNX11	cis	hippocampus	BrainEAC
rs11869625	SNX11	cis	brain	BrainEAC
rs11869625	SNX11	cis	Skin Sun Exposed Lower leg	GTEx
rs11869625	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs11869625	SNX11	cis	temporal cortex	BrainEAC
rs11869625	SNX11	cis	Whole Blood	GTEx
rs11869625	SNX11	cis	frontal cortex	BrainEAC

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46144800-46177800	Weak transcription	Right Ventricle	heart
2	chr17:46147800-46177600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr17:46149000-46178000	Weak transcription	Lung	lung
4	chr17:46154200-46177600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr17:46154400-46177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:46154400-46177600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr17:46154400-46177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:46154400-46177600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:46154400-46177600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:46154400-46177600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:46154400-46177800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:46154600-46177600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr17:46163400-46177600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr17:46163600-46177600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:46163800-46177600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:46163800-46177600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr17:46163800-46177600	Weak transcription	Stomach Mucosa	stomach
18	chr17:46163800-46177800	Weak transcription	Pancreas	Pancrea
19	chr17:46171400-46177600	Weak transcription	Adipose Nuclei	Adipose
20	chr17:46171400-46177800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr17:46171800-46177400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr17:46171800-46177600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr17:46171800-46177600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr17:46171800-46177600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr17:46172000-46177600	Weak transcription	Primary B cells from cord blood	blood
26	chr17:46172000-46177800	Weak transcription	Left Ventricle	heart
27	chr17:46172400-46177800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr17:46172400-46177800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr17:46172400-46177800	Weak transcription	Spleen	Spleen
30	chr17:46172600-46177600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr17:46172800-46177600	Weak transcription	Fetal Intestine Small	intestine
32	chr17:46172800-46177600	Weak transcription	Thymus	Thymus
33	chr17:46173200-46177800	Weak transcription	Esophagus	oesophagus
34	chr17:46173400-46177400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr17:46173400-46177800	Weak transcription	Primary T cells from cord blood	blood
36	chr17:46173600-46177600	Weak transcription	Liver	Liver
37	chr17:46173600-46177600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr17:46173800-46177400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr17:46173800-46177600	Weak transcription	NHDF-Ad	bronchial
40	chr17:46174400-46177400	Weak transcription	Fetal Thymus	thymus
41	chr17:46174400-46177600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr17:46175000-46178000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr17:46175200-46177600	Enhancers	Fetal Heart	heart
44	chr17:46175200-46177800	Enhancers	Colon Smooth Muscle	Colon
45	chr17:46175400-46177600	Enhancers	Fetal Brain Male	brain
46	chr17:46175600-46177600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr17:46175800-46177600	Weak transcription	Brain Anterior Caudate	brain
48	chr17:46175800-46177600	Weak transcription	Brain Substantia Nigra	brain
49	chr17:46175800-46177600	Weak transcription	Fetal Kidney	kidney
50	chr17:46175800-46177600	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links