Variant report

Variant	rs10896012
Chromosome Location	chr11:65278461-65278462
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65083030..65083556-chr11:65278266..65278827,2	MCF-7	breast:
2	chr11:65276130..65278506-chr11:65380000..65382115,2	K562	blood:
3	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:
4	chr11:65275055..65278736-chr11:65316776..65320237,6	K562	blood:
5	chr11:65238496..65239414-chr11:65277511..65278897,3	MCF-7	breast:
6	chr11:65149411..65150020-chr11:65277889..65278844,2	K562	blood:
7	chr11:65183475..65184491-chr11:65277927..65278879,6	K562	blood:
8	chr11:65238647..65239485-chr11:65277894..65278840,4	K562	blood:
9	chr11:65236063..65236580-chr11:65278403..65279025,2	MCF-7	breast:
10	chr11:65183627..65184422-chr11:65277909..65278800,2	MCF-7	breast:
11	chr11:64972361..64972952-chr11:65277885..65278492,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000168056	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000162241	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10896004	0.81[ASN][1000 genomes]
rs10896005	0.83[ASN][1000 genomes]
rs10896006	0.83[ASN][1000 genomes]
rs10896008	0.83[ASN][1000 genomes]
rs10896009	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.83[ASN][1000 genomes]
rs10896010	0.83[ASN][1000 genomes]
rs10896015	0.83[JPT][hapmap];0.82[MEX][hapmap]
rs11227196	0.83[ASN][1000 genomes]
rs11227197	0.83[ASN][1000 genomes]
rs11227198	0.81[ASN][1000 genomes]
rs11227199	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs11227201	0.83[ASN][1000 genomes]
rs11227202	0.83[ASN][1000 genomes]
rs11227205	0.84[ASN][1000 genomes]
rs11227206	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1194076	0.83[JPT][hapmap];0.82[MEX][hapmap]
rs12269965	0.83[ASN][1000 genomes]
rs12269975	0.83[ASN][1000 genomes]
rs12270054	0.83[JPT][hapmap];0.87[MEX][hapmap]
rs12294910	0.83[ASN][1000 genomes]
rs12360896	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs12364730	0.83[ASN][1000 genomes]
rs12788055	0.81[ASN][1000 genomes]
rs12808303	0.81[ASN][1000 genomes]
rs1346	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs17146964	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.83[ASN][1000 genomes]
rs1783541	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap]
rs1787663	0.85[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs2508710	0.83[ASN][1000 genomes]
rs3200401	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs34527830	0.81[ASN][1000 genomes]
rs34582634	0.81[ASN][1000 genomes]
rs34877911	0.83[ASN][1000 genomes]
rs35292734	0.83[ASN][1000 genomes]
rs35469818	0.83[ASN][1000 genomes]
rs35826299	0.83[ASN][1000 genomes]
rs4102217	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7128776	0.83[ASN][1000 genomes]
rs7931615	0.82[ASN][1000 genomes]
rs947791	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
2	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
3	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
4	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS 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	942 gene(s)	inside rSNPs	diseases
5	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
6	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
7	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
8	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
9	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
10	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
11	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
12	nsv541072	chr11:65171202-65313799	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription 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	946 gene(s)	inside rSNPs	diseases
13	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
14	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	961 gene(s)	inside rSNPs	diseases
15	nsv541075	chr11:65210592-65331136	Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	620 gene(s)	inside rSNPs	diseases
16	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
17	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
18	nsv555210	chr11:65266169-65287251	Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	574 gene(s)	inside rSNPs	diseases
19	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
20	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10896012	SNX32	cis	parietal	SCAN
rs10896012	LTBP3	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65270800-65279800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:65275200-65283400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:65275200-65283600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:65275200-65289200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:65275600-65289200	Weak transcription	Fetal Intestine Small	intestine
6	chr11:65276200-65283400	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:65276200-65291600	Weak transcription	Right Atrium	heart
8	chr11:65276400-65283800	Weak transcription	Brain Substantia Nigra	brain
9	chr11:65276400-65289600	Weak transcription	Colon Smooth Muscle	Colon
10	chr11:65276400-65291400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:65277800-65278600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr11:65278000-65278600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr11:65278000-65278600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:65278000-65278600	Enhancers	Brain Anterior Caudate	brain
15	chr11:65278000-65278600	Flanking Active TSS	Hela-S3	cervix
16	chr11:65278000-65278600	Enhancers	HepG2	liver
17	chr11:65278000-65278800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr11:65278000-65278800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr11:65278000-65278800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr11:65278000-65278800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr11:65278000-65278800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr11:65278000-65278800	Enhancers	Dnd41	blood
23	chr11:65278000-65278800	Enhancers	K562	blood
24	chr11:65278200-65278600	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr11:65278400-65279400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr11:65278400-65279600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:65278400-65279600	Weak transcription	Fetal Thymus	thymus
28	chr11:65278400-65283800	Weak transcription	Brain Angular Gyrus	brain
29	chr11:65278400-65284200	Weak transcription	A549	lung
30	chr11:65278400-65289000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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