Variant report

Variant	rs11606656
Chromosome Location	chr11:85524102-85524103
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85374332..85377604-chr11:85518032..85524824,7	MCF-7	breast:
2	chr11:85433132..85435744-chr11:85522806..85525692,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137504	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10898406	0.94[ASN][1000 genomes]
rs10898410	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs10898413	0.92[ASN][1000 genomes]
rs10898414	0.84[ASN][1000 genomes]
rs10898415	0.95[ASN][1000 genomes]
rs11607789	0.85[YRI][hapmap]
rs12362853	0.94[ASN][1000 genomes]
rs1445497	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1481700	0.92[ASN][1000 genomes]
rs17148514	0.85[YRI][hapmap]
rs1893163	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2008890	0.91[ASN][1000 genomes]
rs2044391	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs2044392	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2374683	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs290173	0.87[CHD][hapmap]
rs290190	0.81[CHB][hapmap]
rs290195	0.81[CHB][hapmap]
rs290200	0.83[CHD][hapmap]
rs290202	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs485485	0.91[ASN][1000 genomes]
rs491867	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs493078	0.90[ASN][1000 genomes]
rs4944538	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs496187	0.91[CHB][hapmap];0.90[CHD][hapmap]
rs540063	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs556918	0.94[ASN][1000 genomes]
rs575013	0.83[CHD][hapmap]
rs589327	0.90[CHB][hapmap]
rs630613	0.86[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs631410	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs644972	0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs647912	0.91[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs652615	0.90[ASN][1000 genomes]
rs667275	0.90[ASN][1000 genomes]
rs679204	0.91[CHB][hapmap]
rs680498	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs683105	0.90[ASN][1000 genomes]
rs7103790	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7123846	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11606656	SYTL2	cis	cerebellum	SCAN
rs11606656	INO80D	trans	cerebellum	SCAN
rs11606656	SYTL2	cis	multi-tissue	Pritchard
rs11606656	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85521600-85525000	Weak transcription	Hela-S3	cervix
2	chr11:85522600-85525000	Weak transcription	Fetal Brain Male	brain
3	chr11:85522600-85525800	Weak transcription	HMEC	breast
4	chr11:85522600-85527000	Enhancers	Stomach Mucosa	stomach
5	chr11:85522600-85533200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:85522800-85524400	Weak transcription	Small Intestine	intestine
7	chr11:85522800-85524400	Weak transcription	NHLF	lung
8	chr11:85522800-85525000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:85522800-85525200	Weak transcription	NHDF-Ad	bronchial
10	chr11:85522800-85525600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:85522800-85525600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:85522800-85525600	Weak transcription	HSMM	muscle
13	chr11:85522800-85525800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:85522800-85525800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:85522800-85525800	Weak transcription	NH-A	brain
16	chr11:85522800-85525800	Weak transcription	NHEK	skin
17	chr11:85522800-85526200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:85522800-85526200	Weak transcription	Primary T cells from cord blood	blood
19	chr11:85522800-85526200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr11:85523000-85524400	Weak transcription	Fetal Intestine Large	intestine
21	chr11:85523000-85524400	Weak transcription	A549	lung
22	chr11:85523000-85524800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:85523000-85525000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:85523000-85525000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr11:85523000-85525400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:85523000-85526600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr11:85523000-85526600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr11:85523000-85526600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr11:85523400-85528400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr11:85523600-85524400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:85523600-85524600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr11:85523800-85524200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr11:85523800-85526200	Enhancers	Duodenum Mucosa	Duodenum
34	chr11:85523800-85526800	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr11:85524000-85526000	Enhancers	Fetal Intestine Small	intestine

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