Variant report

Variant	rs722823
Chromosome Location	chr11:57302568-57302569
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	chr11:57298163..57300206-chr11:57300287..57302830,3	K562	blood:

Variant related genes	Relation type
ENSG00000134809	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10896623	0.81[LWK][hapmap]
rs1124942	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12223229	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2234409	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2467328	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2467329	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2467330	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581930	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2649644	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2649645	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2649649	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2649651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2649653	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2649655	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2649656	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2649658	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2649659	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2649666	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2729358	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729359	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729367	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2729368	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2729369	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2729370	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2729373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2729375	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2729382	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848621	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848622	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2848624	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848638	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4939148	0.81[LWK][hapmap]
rs514385	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs722823	SLC43A1	cis	parietal	SCAN
rs722823	SLC43A3	cis	cerebellum	SCAN
rs722823	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs722823	DTX4	cis	cerebellum	SCAN
rs722823	SMTNL1	cis	Artery Tibial	GTEx
rs722823	SMTNL1	cis	lymphoblastoid	seeQTL
rs722823	SMTNL1	cis	Thyroid	GTEx
rs722823	SMTNL1	cis	Esophagus Muscularis	GTEx
rs722823	SMTNL1	cis	lung	GTEx
rs722823	SMTNL1	cis	Nerve Tibial	GTEx
rs722823	MS4A5	cis	cerebellum	SCAN
rs722823	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs722823	OR5J2	cis	parietal	SCAN
rs722823	UBE2L6	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57298400-57304400	Weak transcription	Spleen	Spleen
2	chr11:57298800-57319200	Weak transcription	Small Intestine	intestine
3	chr11:57299000-57304400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:57299000-57304600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:57299000-57305800	Weak transcription	Lung	lung
6	chr11:57299000-57310200	Weak transcription	Right Ventricle	heart
7	chr11:57299000-57314000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:57299000-57317000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:57299000-57317200	Weak transcription	Colon Smooth Muscle	Colon
10	chr11:57299000-57317400	Weak transcription	Fetal Brain Male	brain
11	chr11:57299200-57304200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:57299200-57304200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr11:57299200-57304400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:57299200-57304400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr11:57299200-57305200	Weak transcription	Brain Germinal Matrix	brain
16	chr11:57299200-57305600	Weak transcription	Fetal Brain Female	brain
17	chr11:57299200-57307000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:57299200-57307000	Weak transcription	Thymus	Thymus
19	chr11:57299200-57313600	Weak transcription	Fetal Thymus	thymus
20	chr11:57299200-57314200	Weak transcription	Brain Hippocampus Middle	brain
21	chr11:57299200-57314800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:57299200-57316200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr11:57299200-57317200	Weak transcription	Brain Angular Gyrus	brain
24	chr11:57299200-57333000	Weak transcription	Right Atrium	heart
25	chr11:57299400-57304000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:57299400-57304400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:57299400-57304400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:57299400-57306200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:57299400-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr11:57299400-57313600	Weak transcription	Liver	Liver
31	chr11:57299400-57314000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr11:57299400-57314000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr11:57299400-57314000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr11:57299400-57314000	Weak transcription	GM12878-XiMat	blood
35	chr11:57299400-57314200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr11:57299400-57317200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr11:57299600-57306800	Weak transcription	NHEK	skin
38	chr11:57299800-57305800	Weak transcription	Primary T cells from cord blood	blood
39	chr11:57299800-57306800	Weak transcription	Dnd41	blood
40	chr11:57300000-57310600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr11:57300000-57313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr11:57300200-57306400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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