Variant report

Variant	rs10896623
Chromosome Location	chr11:57295864-57295865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57224304..57226625-chr11:57294106..57296478,4	K562	blood:
2	chr11:57292477..57296508-chr11:57296772..57299777,9	K562	blood:
3	chr11:57294684..57296803-chr11:57368353..57370314,2	K562	blood:
4	chr11:57294879..57296501-chr11:57296689..57299777,3	K562	blood:
5	chr11:57294877..57297638-chr11:57477867..57480575,2	K562	blood:
6	chr11:57226906..57228530-chr11:57293976..57296278,2	K562	blood:
7	chr11:57225517..57229165-chr11:57295790..57298188,3	K562	blood:
8	chr11:57293312..57295959-chr11:57408961..57411007,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000186907	Chromatin interaction
ENSG00000213593	Chromatin interaction
ENSG00000149131	Chromatin interaction
ENSG00000254462	Chromatin interaction
ENSG00000156603	Chromatin interaction
ENSG00000134809	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10792101	0.83[ASW][hapmap]
rs12277281	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3758921	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3851118	0.85[CEU][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4938869	0.89[ASW][hapmap]
rs4938870	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4939148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7109985	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7110678	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs722823	0.81[LWK][hapmap]
rs7925116	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10896623	P2RX3	cis	parietal	SCAN
rs10896623	TIMM10	cis	cerebellum	SCAN
rs10896623	TIMM10	cis	multi-tissue	Pritchard
rs10896623	TIMM10	cis	brain	seeQTL
rs10896623	SMTNL1	cis	Artery Tibial	GTEx
rs10896623	TIMM10	cis	Artery Tibial	GTEx
rs10896623	TIMM10	cis	lung	GTEx
rs10896623	MS4A5	cis	cerebellum	SCAN
rs10896623	TIMM10	cis	Esophagus Muscularis	GTEx
rs10896623	SLC43A1	cis	cerebellum	SCAN
rs10896623	OR8K5	cis	cerebellum	SCAN
rs10896623	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs10896623	OR5J2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57283400-57297400	Weak transcription	Gastric	stomach
2	chr11:57283600-57296000	Weak transcription	Spleen	Spleen
3	chr11:57283600-57296200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:57283800-57296000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr11:57283800-57296000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr11:57283800-57296000	Weak transcription	Left Ventricle	heart
7	chr11:57283800-57296200	Weak transcription	HSMM	muscle
8	chr11:57283800-57296400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:57283800-57296600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:57283800-57296600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:57283800-57297000	Weak transcription	Brain Angular Gyrus	brain
12	chr11:57283800-57297200	Weak transcription	Fetal Lung	lung
13	chr11:57283800-57297200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:57283800-57297200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:57283800-57297200	Weak transcription	Right Atrium	heart
16	chr11:57283800-57297200	Weak transcription	NH-A	brain
17	chr11:57283800-57297400	Weak transcription	Colonic Mucosa	Colon
18	chr11:57283800-57297400	Weak transcription	HSMMtube	muscle
19	chr11:57284000-57296000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:57284000-57296000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:57284000-57296000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:57284000-57296000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:57284000-57297000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:57284000-57297000	Weak transcription	NHDF-Ad	bronchial
25	chr11:57284400-57296000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:57284800-57297000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr11:57285400-57296200	Weak transcription	Primary B cells from cord blood	blood
28	chr11:57286600-57297200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:57287600-57297200	Weak transcription	Fetal Brain Male	brain
30	chr11:57290200-57297400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr11:57292400-57296200	Strong transcription	Fetal Brain Female	brain
32	chr11:57292600-57296000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:57292600-57296200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:57292600-57296200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:57292600-57297400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:57292600-57297600	Weak transcription	Aorta	Aorta
37	chr11:57292800-57296400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr11:57292800-57297000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr11:57292800-57297000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:57292800-57297200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:57293000-57296000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:57293000-57296600	Weak transcription	Brain Germinal Matrix	brain
43	chr11:57293000-57297000	Weak transcription	Small Intestine	intestine
44	chr11:57293000-57297200	Weak transcription	Brain Hippocampus Middle	brain
45	chr11:57293000-57297200	Weak transcription	Brain Substantia Nigra	brain
46	chr11:57293200-57297200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:57293600-57297400	Weak transcription	Ovary	ovary
48	chr11:57293800-57296200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:57293800-57296400	Strong transcription	HUVEC	blood vessel
50	chr11:57294000-57296200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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