Variant report

Variant	rs10896043
Chromosome Location	chr11:65543827-65543828
allele	C/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: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	chr11:65463670..65466251-chr11:65542574..65544907,2	K562	blood:
2	chr11:65543427..65545699-chr11:65553681..65556951,3	K562	blood:
3	chr11:65526354..65531692-chr11:65541770..65544711,4	K562	blood:
4	chr11:65542483..65544503-chr11:65618278..65620229,2	K562	blood:
5	chr11:65541717..65544570-chr11:65625545..65627140,2	MCF-7	breast:
6	chr11:65542929..65545137-chr11:65617761..65620123,2	K562	blood:
7	chr11:65543425..65544156-chr11:65585413..65586242,2	MCF-7	breast:
8	chr11:65487099..65491310-chr11:65543476..65547938,6	MCF-7	breast:
9	chr11:65509847..65512521-chr11:65541079..65543934,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172757	Chromatin interaction
ENSG00000172818	Chromatin interaction
ENSG00000172922	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11227261	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs11227283	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11227284	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227288	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227303	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1151488	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs1193851	0.85[CHB][hapmap]
rs1205259	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs12273982	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12287832	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1784223	0.85[CHB][hapmap]
rs1787034	0.85[CHB][hapmap];0.94[CHD][hapmap]
rs3372	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs4930304	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs494003	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578056	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7122657	0.85[CHB][hapmap]
rs7944860	0.85[CHB][hapmap];0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
4	nsv897758	chr11:65490756-65564035	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv897759	chr11:65543827-65554502	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10896043	IZUMO2	trans	parietal	SCAN
rs10896043	RNASEH2C	cis	lymphoblastoid	seeQTL
rs10896043	SIPA1	cis	cerebellum	SCAN
rs10896043	SNX32	cis	parietal	SCAN
rs10896043	SNX32	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65532600-65544000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr11:65534200-65544600	Weak transcription	Osteobl	bone
3	chr11:65537400-65544200	Weak transcription	NHLF	lung
4	chr11:65537400-65544400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr11:65537400-65544400	Weak transcription	Dnd41	blood
6	chr11:65537400-65544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr11:65537400-65544600	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:65537400-65544600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr11:65537400-65544800	Weak transcription	Brain Hippocampus Middle	brain
10	chr11:65537400-65545200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr11:65537400-65546600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr11:65537400-65546600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:65537600-65544200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:65537600-65545000	Weak transcription	Aorta	Aorta
15	chr11:65537600-65546600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr11:65537800-65546800	Weak transcription	K562	blood
17	chr11:65538800-65544400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:65539000-65544200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:65539000-65544200	Weak transcription	Gastric	stomach
20	chr11:65539000-65544400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:65539600-65546600	Weak transcription	Stomach Mucosa	stomach
22	chr11:65540200-65544800	Weak transcription	HUVEC	blood vessel
23	chr11:65540600-65544200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr11:65540600-65545800	Weak transcription	Brain Substantia Nigra	brain
25	chr11:65540800-65544200	Weak transcription	Brain Germinal Matrix	brain
26	chr11:65541000-65544200	Weak transcription	Fetal Thymus	thymus
27	chr11:65541200-65544400	Weak transcription	Fetal Brain Female	brain
28	chr11:65541200-65544600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:65541400-65544600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr11:65541600-65544200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:65541800-65544000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr11:65541800-65544800	Enhancers	Pancreas	Pancrea
33	chr11:65542000-65544000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr11:65542000-65544800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:65542000-65546400	Strong transcription	Fetal Intestine Small	intestine
36	chr11:65542200-65544200	Weak transcription	Fetal Muscle Leg	muscle
37	chr11:65542200-65545200	Strong transcription	Hela-S3	cervix
38	chr11:65542200-65545600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:65542200-65546000	Strong transcription	Brain Anterior Caudate	brain
40	chr11:65542200-65546200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr11:65542200-65546600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:65542200-65547000	Strong transcription	A549	lung
43	chr11:65542400-65544000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:65542400-65544200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:65542400-65544200	Enhancers	Adipose Nuclei	Adipose
46	chr11:65542400-65545000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:65542400-65545200	Strong transcription	Stomach Smooth Muscle	stomach
48	chr11:65542400-65545400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:65542400-65545600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr11:65542400-65545800	Strong transcription	Brain Cingulate Gyrus	brain

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