Variant report

Variant	rs2649658
Chromosome Location	chr11:57313659-57313660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57312168..57315118-chr11:57412878..57415826,2	K562	blood:
2	chr11:57308278..57310197-chr11:57313267..57314907,2	K562	blood:
3	chr11:57299281..57301007-chr11:57311388..57313824,2	K562	blood:
4	chr11:57298175..57301007-chr11:57311281..57313824,2	K562	blood:

Variant related genes	Relation type
ENSG00000254602	Chromatin interaction
ENSG00000214872	Chromatin interaction
ENSG00000134809	Chromatin interaction
ENSG00000166793	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1124942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12223229	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2234409	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2467328	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2467329	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2467330	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2581930	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2649644	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2649645	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2649649	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649651	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649653	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2649655	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2649656	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649666	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2729358	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2729359	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2729367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729368	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2729369	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729370	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729373	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729375	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729382	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2848621	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2848622	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2848624	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2848638	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2848639	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs514385	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs722823	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1051032	chr11:57290124-57363064	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv541049	chr11:57290124-57363064	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1052073	chr11:57297499-57362802	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv541050	chr11:57297499-57362802	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2649658	SMTNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs2649658	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs2649658	SMTNL1	cis	Esophagus Muscularis	GTEx
rs2649658	SMTNL1	cis	lung	GTEx
rs2649658	SMTNL1	cis	Thyroid	GTEx
rs2649658	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2649658	SMTNL1	cis	Nerve Tibial	GTEx
rs2649658	SMTNL1	cis	Artery Tibial	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57298800-57319200	Weak transcription	Small Intestine	intestine
2	chr11:57299000-57314000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr11:57299000-57317000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:57299000-57317200	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:57299000-57317400	Weak transcription	Fetal Brain Male	brain
6	chr11:57299200-57314200	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:57299200-57314800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:57299200-57316200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:57299200-57317200	Weak transcription	Brain Angular Gyrus	brain
10	chr11:57299200-57333000	Weak transcription	Right Atrium	heart
11	chr11:57299400-57314000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr11:57299400-57314000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr11:57299400-57314000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr11:57299400-57314000	Weak transcription	GM12878-XiMat	blood
15	chr11:57299400-57314200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:57299400-57317200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:57304800-57314800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:57306000-57315000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:57306800-57315000	Weak transcription	Gastric	stomach
20	chr11:57307200-57314600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:57307200-57333600	Weak transcription	HMEC	breast
22	chr11:57307400-57314000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr11:57307400-57314600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr11:57307800-57314000	Weak transcription	Primary T cells from cord blood	blood
25	chr11:57308000-57314000	Weak transcription	Brain Anterior Caudate	brain
26	chr11:57309200-57333400	Weak transcription	Psoas Muscle	Psoas
27	chr11:57310800-57314400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:57310800-57319200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:57311000-57317000	Weak transcription	Fetal Lung	lung
30	chr11:57311200-57316200	Weak transcription	Esophagus	oesophagus
31	chr11:57311200-57316600	Weak transcription	Aorta	Aorta
32	chr11:57311400-57314000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:57311400-57314000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr11:57311400-57315200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr11:57311400-57316200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr11:57311400-57317200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr11:57311400-57317200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr11:57311400-57317200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:57311400-57319800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr11:57311400-57320400	Weak transcription	Stomach Mucosa	stomach
41	chr11:57311600-57314000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:57311600-57314000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr11:57311600-57314600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr11:57311600-57314800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:57311600-57314800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:57311600-57316800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:57311600-57317000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:57311600-57317200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr11:57311600-57317200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr11:57311600-57319400	Weak transcription	Right Ventricle	heart

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