Variant report

Variant	rs12223229
Chromosome Location	chr11:57313469-57313470
allele	C/G
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
ENSG00000214872	Chromatin interaction
ENSG00000166793	Chromatin interaction
ENSG00000134809	Chromatin interaction
ENSG00000254602	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	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2234409	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2467328	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2467329	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2467330	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2581930	0.85[EUR][1000 genomes]
rs2649644	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2649645	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2649649	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649651	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649653	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2649655	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2649656	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649658	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2649659	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649666	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2729358	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2729359	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2729367	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729368	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2729369	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729370	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729373	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729375	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2729382	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2848621	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2848622	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2848624	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2848638	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2848639	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs514385	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs722823	0.89[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
rs12223229	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs12223229	SMTNL1	cis	Esophagus Muscularis	GTEx
rs12223229	SMTNL1	cis	lung	GTEx
rs12223229	SMTNL1	cis	Thyroid	GTEx
rs12223229	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs12223229	SMTNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs12223229	SMTNL1	cis	Artery Tibial	GTEx
rs12223229	SMTNL1	cis	Nerve Tibial	GTEx

Chromatin state (count:94 , 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	chr11:57299200-57313600	Weak transcription	Fetal Thymus	thymus
7	chr11:57299200-57314200	Weak transcription	Brain Hippocampus Middle	brain
8	chr11:57299200-57314800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:57299200-57316200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr11:57299200-57317200	Weak transcription	Brain Angular Gyrus	brain
11	chr11:57299200-57333000	Weak transcription	Right Atrium	heart
12	chr11:57299400-57313600	Weak transcription	Liver	Liver
13	chr11:57299400-57314000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:57299400-57314000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr11:57299400-57314000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr11:57299400-57314000	Weak transcription	GM12878-XiMat	blood
17	chr11:57299400-57314200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr11:57299400-57317200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:57304800-57314800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:57306000-57313600	Weak transcription	Lung	lung
21	chr11:57306000-57315000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:57306800-57315000	Weak transcription	Gastric	stomach
23	chr11:57307200-57314600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr11:57307200-57333600	Weak transcription	HMEC	breast
25	chr11:57307400-57314000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr11:57307400-57314600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr11:57307600-57313600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:57307800-57314000	Weak transcription	Primary T cells from cord blood	blood
29	chr11:57308000-57313600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:57308000-57314000	Weak transcription	Brain Anterior Caudate	brain
31	chr11:57309200-57333400	Weak transcription	Psoas Muscle	Psoas
32	chr11:57310800-57314400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:57310800-57319200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:57311000-57313600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:57311000-57317000	Weak transcription	Fetal Lung	lung
36	chr11:57311200-57316200	Weak transcription	Esophagus	oesophagus
37	chr11:57311200-57316600	Weak transcription	Aorta	Aorta
38	chr11:57311400-57313600	Strong transcription	Fetal Muscle Leg	muscle
39	chr11:57311400-57314000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:57311400-57314000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr11:57311400-57315200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr11:57311400-57316200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr11:57311400-57317200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr11:57311400-57317200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:57311400-57317200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr11:57311400-57319800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr11:57311400-57320400	Weak transcription	Stomach Mucosa	stomach
48	chr11:57311600-57314000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:57311600-57314000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr11:57311600-57314600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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