Variant report

Variant	rs630613
Chromosome Location	chr11:85478997-85478998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85467154..85470617-chr11:85475521..85479674,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10898406	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10898410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10898413	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898414	0.81[ASN][1000 genomes]
rs10898415	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11604141	0.86[CEU][hapmap]
rs11606656	0.86[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12362853	0.92[ASN][1000 genomes]
rs1445497	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1445513	0.82[CEU][hapmap]
rs1481700	0.97[ASN][1000 genomes]
rs1893163	0.83[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2008890	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2044391	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2044392	0.85[ASN][1000 genomes]
rs2374683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs370385	0.82[JPT][hapmap]
rs475380	0.80[ASN][1000 genomes]
rs478089	0.82[ASN][1000 genomes]
rs485485	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs491867	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs493078	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944538	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs496187	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs520500	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs540063	0.81[CHB][hapmap]
rs550404	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs556669	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs556918	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs580459	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs589327	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs597480	0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs631410	0.86[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs641393	0.82[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs644972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647912	0.86[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs652615	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs667275	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs678723	0.82[ASN][1000 genomes]
rs679204	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs680498	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs683105	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689093	0.80[ASN][1000 genomes]
rs7103790	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7123846	0.86[AMR][1000 genomes];0.93[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	nsv898050	chr11:85406915-85499290	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv555639	chr11:85436352-85495269	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs630613	SYTL2	cis	Nerve Tibial	GTEx
rs630613	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85430400-85480400	Weak transcription	Aorta	Aorta
2	chr11:85448000-85480600	Weak transcription	Fetal Stomach	stomach
3	chr11:85460600-85483800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:85469400-85485400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:85471800-85482600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:85471800-85483200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:85472000-85480600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:85472000-85481200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr11:85472000-85485400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr11:85472600-85484600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr11:85474000-85487400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:85475200-85481000	Weak transcription	Primary T cells from cord blood	blood
13	chr11:85475600-85488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:85476000-85482400	Weak transcription	HSMM	muscle
15	chr11:85477000-85479400	Enhancers	Duodenum Mucosa	Duodenum
16	chr11:85477400-85479000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr11:85477800-85479000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr11:85477800-85479400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr11:85478200-85479400	Enhancers	Stomach Mucosa	stomach
20	chr11:85478200-85486200	Weak transcription	Small Intestine	intestine
21	chr11:85478400-85480200	Enhancers	Fetal Kidney	kidney
22	chr11:85478400-85480400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:85478600-85479000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:85478600-85479000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:85478600-85479200	Enhancers	NHDF-Ad	bronchial
26	chr11:85478600-85480400	Weak transcription	Fetal Intestine Small	intestine
27	chr11:85478600-85483400	Weak transcription	NHLF	lung
28	chr11:85478600-85486200	Weak transcription	Colonic Mucosa	Colon
29	chr11:85478800-85479000	Enhancers	GM12878-XiMat	blood
30	chr11:85478800-85479400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:85478800-85480000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr11:85478800-85484000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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