Variant report

Variant	rs290196
Chromosome Location	chr11:85416303-85416304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr11:85416043-85416320	K562	blood:	n/a	n/a
2	MAFK	chr11:85416054-85416354	HepG2	liver:	n/a	n/a
3	MAFF	chr11:85416050-85416372	K562	blood:	n/a	chr11:85416204-85416222
4	POLR2A	chr11:85415451-85417071	K562	blood:	n/a	n/a
5	MAFK	chr11:85416056-85416349	Hela-S3	cervix:	n/a	n/a
6	MAFK	chr11:85416035-85416385	HepG2	liver:	n/a	n/a
7	MAFK	chr11:85416051-85416373	IMR90	lung:	n/a	n/a
8	MAFF	chr11:85416039-85416367	HepG2	liver:	n/a	chr11:85416204-85416222

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85374847..85376948-chr11:85415387..85418277,3	K562	blood:
2	chr11:85409414..85413746-chr11:85414065..85417765,4	K562	blood:

Variant related genes	Relation type
SYTL2	TF binding region
ENSG00000137504	Chromatin interaction
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10501595	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs11234359	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs11234410	0.84[EUR][1000 genomes]
rs11604141	0.81[JPT][hapmap]
rs1192	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs1214001	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12419172	0.94[JPT][hapmap]
rs1354397	0.84[CHB][hapmap]
rs1445513	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs17208492	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs17208519	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs17810659	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs188311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1892872	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs1991923	0.94[JPT][hapmap]
rs2290823	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2467059	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs290172	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290173	0.80[CEU][hapmap]
rs290175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs290177	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs290178	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs290182	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs290185	0.83[YRI][hapmap]
rs290186	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs290190	0.88[CEU][hapmap]
rs290194	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290197	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290199	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290200	0.87[CEU][hapmap]
rs290202	0.88[CEU][hapmap]
rs370385	0.80[YRI][hapmap]
rs487964	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs489896	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs491867	0.83[CEU][hapmap]
rs493673	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4943925	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4944529	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4944531	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs496187	0.83[CEU][hapmap]
rs510948	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap]
rs520629	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs521764	0.84[EUR][1000 genomes]
rs537266	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs537604	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs540063	0.87[CEU][hapmap]
rs550404	0.87[CEU][hapmap]
rs556669	0.88[CEU][hapmap]
rs558377	0.92[EUR][1000 genomes]
rs56579	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs573766	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs578324	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs580459	0.87[CEU][hapmap]
rs583122	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs589327	0.87[CEU][hapmap]
rs592380	0.92[EUR][1000 genomes]
rs592712	0.95[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap]
rs597480	0.83[CEU][hapmap]
rs609012	0.87[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap]
rs613973	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs631104	0.80[EUR][1000 genomes]
rs631410	0.84[CEU][hapmap]
rs639688	0.95[CEU][hapmap];0.88[JPT][hapmap]
rs641393	0.83[CEU][hapmap]
rs644972	0.84[CEU][hapmap]
rs647912	0.83[CEU][hapmap]
rs650036	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs650970	0.81[EUR][1000 genomes]
rs653559	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs679204	0.87[CEU][hapmap]
rs680498	0.91[CEU][hapmap]
rs681044	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs688741	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7119617	0.90[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]
rs7943586	0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap]
rs7948778	0.85[CHB][hapmap]
rs881121	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs947861	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs947863	0.90[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs290196	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85394000-85427400	Weak transcription	Small Intestine	intestine
2	chr11:85396800-85429800	Weak transcription	Stomach Mucosa	stomach
3	chr11:85397000-85417400	Weak transcription	Gastric	stomach
4	chr11:85397000-85418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:85397000-85425400	Weak transcription	Lung	lung
6	chr11:85397200-85438600	Weak transcription	Colonic Mucosa	Colon
7	chr11:85397600-85422000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:85397600-85428400	Weak transcription	Brain Angular Gyrus	brain
9	chr11:85397800-85421600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:85397800-85430000	Weak transcription	Ovary	ovary
11	chr11:85398000-85427600	Weak transcription	Brain Substantia Nigra	brain
12	chr11:85405000-85418200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:85406200-85429800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:85406600-85416800	Weak transcription	NH-A	brain
15	chr11:85407000-85416400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:85408600-85426600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:85409000-85421800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:85409000-85425200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:85409400-85418200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr11:85409400-85427200	Weak transcription	Fetal Lung	lung
21	chr11:85410600-85424400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr11:85411000-85417400	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:85411800-85424800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr11:85412000-85417400	Weak transcription	Primary T cells from cord blood	blood
25	chr11:85412000-85436800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr11:85412000-85438000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:85412600-85427000	Weak transcription	Fetal Intestine Small	intestine
28	chr11:85413600-85416400	Weak transcription	HSMMtube	muscle
29	chr11:85413600-85417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:85413600-85417200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:85413600-85427200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:85413600-85429600	Weak transcription	Fetal Stomach	stomach
33	chr11:85413800-85416800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:85413800-85417400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr11:85413800-85417600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:85413800-85418200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:85413800-85430000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:85415600-85417000	Strong transcription	NHLF	lung
39	chr11:85416000-85417200	Enhancers	A549	lung
40	chr11:85416000-85417600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:85416200-85417000	Enhancers	NHDF-Ad	bronchial
42	chr11:85416200-85417800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:85416200-85417800	Genic enhancers	HSMM	muscle

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