Variant report

Variant	rs290193
Chromosome Location	chr11:85429074-85429075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85428619..85430275-chr11:85519411..85522192,2	MCF-7	breast:
2	chr11:85427809..85429920-chr11:85433567..85435878,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1237203	0.82[JPT][hapmap]
rs1893163	0.84[LWK][hapmap];0.83[MEX][hapmap]
rs290171	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs290173	0.88[ASW][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.86[ASN][1000 genomes]
rs290174	0.86[ASN][1000 genomes]
rs290179	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs290180	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs290183	0.81[CHB][hapmap]
rs290185	0.82[JPT][hapmap]
rs290190	0.87[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs290191	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs290195	0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs290198	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs290200	0.88[ASW][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs290201	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs290202	0.88[ASW][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.90[ASN][1000 genomes]
rs431606	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs491867	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs496187	0.87[CHD][hapmap]
rs540063	0.85[CHD][hapmap]
rs570394	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs575013	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs575050	0.86[CHB][hapmap]
rs597480	0.85[LWK][hapmap]
rs623120	0.84[EUR][1000 genomes]
rs641393	0.85[LWK][hapmap]
rs647912	0.87[CHD][hapmap]
rs678376	0.83[ASW][hapmap];0.84[LWK][hapmap];0.92[YRI][hapmap]
rs680498	0.85[CHD][hapmap]
rs7103790	0.80[LWK][hapmap]

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	nsv468768	chr11:85395180-85436352	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv555632	chr11:85395180-85436352	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv1052123	chr11:85425856-85471132	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking 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
10	nsv555633	chr11:85426330-85473883	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription 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
11	nsv1036110	chr11:85429074-85471132	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1054027	chr11:85429074-85477283	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs290193	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85396800-85429800	Weak transcription	Stomach Mucosa	stomach
2	chr11:85397200-85438600	Weak transcription	Colonic Mucosa	Colon
3	chr11:85397800-85430000	Weak transcription	Ovary	ovary
4	chr11:85406200-85429800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:85412000-85436800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:85412000-85438000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr11:85413600-85429600	Weak transcription	Fetal Stomach	stomach
8	chr11:85413800-85430000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:85417600-85453000	Weak transcription	Gastric	stomach
10	chr11:85418400-85436400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr11:85422400-85430200	Weak transcription	Fetal Kidney	kidney
12	chr11:85422600-85448600	Weak transcription	Fetal Intestine Large	intestine
13	chr11:85422800-85448200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr11:85423000-85429800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:85423600-85430000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:85424000-85448600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:85424600-85429800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:85425600-85429600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:85425600-85429800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr11:85425800-85429600	Weak transcription	Primary T cells from cord blood	blood
21	chr11:85425800-85429600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:85427000-85430600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr11:85427200-85429600	Active TSS	Fetal Muscle Leg	muscle
24	chr11:85427200-85430200	Active TSS	NHLF	lung
25	chr11:85427200-85430600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:85427200-85430600	Active TSS	Fetal Muscle Trunk	muscle
27	chr11:85427200-85433000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:85427400-85430600	Active TSS	HSMMtube	muscle
29	chr11:85427600-85429600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:85427600-85429600	Active TSS	NH-A	brain
31	chr11:85427600-85429800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr11:85427600-85430400	Active TSS	NHDF-Ad	bronchial
33	chr11:85427800-85429200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:85427800-85429600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:85427800-85429800	Weak transcription	Psoas Muscle	Psoas
36	chr11:85427800-85430000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr11:85427800-85430600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:85428200-85430600	Active TSS	HSMM	muscle
39	chr11:85428400-85429600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:85428400-85429600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:85428400-85430200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:85428400-85430600	Active TSS	Brain Angular Gyrus	brain
43	chr11:85428600-85429400	Enhancers	Osteobl	bone
44	chr11:85428600-85429600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr11:85428600-85429600	Enhancers	Brain Cingulate Gyrus	brain
46	chr11:85428600-85429800	Flanking Active TSS	A549	lung
47	chr11:85428600-85430000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:85428600-85430800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr11:85428600-85431000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr11:85428600-85432000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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