Variant report

Variant	rs895255
Chromosome Location	chr11:85534546-85534547
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85371590..85374337-chr11:85533761..85535613,2	MCF-7	breast:
2	chr11:85446235..85448098-chr11:85532932..85535818,2	MCF-7	breast:
3	chr11:85371076..85377725-chr11:85533880..85541610,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137504	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10898417	0.85[GIH][hapmap]
rs11234420	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234457	0.86[GIH][hapmap]
rs11234462	1.00[GIH][hapmap]
rs12271536	0.82[GIH][hapmap]
rs12361800	0.86[CEU][hapmap];1.00[GIH][hapmap]
rs1445499	0.84[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs1564550	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36093844	0.86[CEU][hapmap];0.96[GIH][hapmap]
rs7101889	0.96[GIH][hapmap]
rs7102361	0.81[CEU][hapmap]
rs7113656	0.96[GIH][hapmap]
rs7124956	0.96[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv832222	chr11:85405712-85603981	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1047147	chr11:85459235-85594800	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv541114	chr11:85459235-85594800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv2762927	chr11:85468051-85559618	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1052737	chr11:85477084-85554914	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv541115	chr11:85477084-85554914	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1049630	chr11:85486866-85535123	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
13	nsv1048818	chr11:85524635-85746473	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
14	nsv541116	chr11:85524635-85746473	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs895255	RAB30	cis	cerebellum	SCAN
rs895255	SYTL2	cis	lymphoblastoid	seeQTL
rs895255	FZD4	cis	cerebellum	SCAN
rs895255	SYTL2	cis	parietal	SCAN
rs895255	SYTL2	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85524800-85537200	Weak transcription	Small Intestine	intestine
2	chr11:85531000-85535000	Weak transcription	Fetal Lung	lung
3	chr11:85532000-85535400	Enhancers	Stomach Mucosa	stomach
4	chr11:85532400-85535200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:85532400-85538800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr11:85532400-85540000	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr11:85532600-85534600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr11:85532600-85535400	Enhancers	NHDF-Ad	bronchial
9	chr11:85532600-85539200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr11:85532600-85539600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:85532800-85535200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr11:85532800-85535400	Enhancers	NHLF	lung
13	chr11:85532800-85536200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:85532800-85539200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr11:85532800-85540000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:85533000-85537200	Weak transcription	Hela-S3	cervix
17	chr11:85533200-85535400	Enhancers	A549	lung
18	chr11:85533200-85536800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:85533200-85538400	Weak transcription	NH-A	brain
20	chr11:85533200-85539800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:85533400-85538400	Weak transcription	Pancreas	Pancrea
22	chr11:85533600-85535400	Enhancers	HSMMtube	muscle
23	chr11:85533800-85534600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:85534000-85534600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr11:85534000-85535200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:85534000-85537000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr11:85534000-85537200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:85534000-85537200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr11:85534000-85537400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr11:85534200-85534600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:85534200-85535000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr11:85534200-85535400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr11:85534200-85535400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:85534200-85535400	Enhancers	Dnd41	blood
35	chr11:85534200-85535600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:85534200-85536800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr11:85534200-85537400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:85534200-85537400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:85534200-85537400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr11:85534200-85537600	Weak transcription	Osteobl	bone
41	chr11:85534200-85538200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:85534400-85534800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr11:85534400-85534800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:85534400-85535400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr11:85534400-85535600	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr11:85534400-85536600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:85534400-85536800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr11:85534400-85537000	Weak transcription	HSMM	muscle
49	chr11:85534400-85537400	Weak transcription	HMEC	breast

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