Variant report

Variant	rs4917589
Chromosome Location	chr10:112612802-112612803
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:112612328..112615188-chr10:112618146..112620341,2	MCF-7	breast:
2	chr10:112606555..112610300-chr10:112611947..112614972,3	MCF-7	breast:
3	chr10:112608440..112622028-chr10:112627331..112635995,26	MCF-7	breast:
4	chr10:112602080..112604237-chr10:112611419..112615912,4	K562	blood:
5	chr10:112610748..112613703-chr10:112623981..112626805,2	MCF-7	breast:
6	chr10:112612441..112615038-chr10:112661869..112664836,2	K562	blood:
7	chr10:112604056..112607553-chr10:112607737..112614942,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150593	Chromatin interaction
ENSG00000232470	Chromatin interaction
ENSG00000214413	Chromatin interaction
ENSG00000203497	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10787286	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10787291	1.00[JPT][hapmap]
rs10885059	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10885060	0.86[ASN][1000 genomes]
rs10885075	0.95[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs11195391	1.00[JPT][hapmap]
rs12240685	0.80[ASN][1000 genomes]
rs12256157	1.00[CHB][hapmap]
rs12261765	0.80[ASN][1000 genomes]
rs12572941	1.00[CHB][hapmap]
rs12776861	0.80[ASN][1000 genomes]
rs12783690	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1322997	0.90[GIH][hapmap]
rs1571239	0.81[EUR][1000 genomes]
rs1927159	0.88[TSI][hapmap]
rs2146544	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34401279	0.80[ASN][1000 genomes]
rs35394459	0.86[ASN][1000 genomes]
rs35793075	0.80[ASN][1000 genomes]
rs35946882	0.86[ASN][1000 genomes]
rs3750619	1.00[JPT][hapmap]
rs3763692	0.86[ASN][1000 genomes]
rs6421360	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6585018	0.90[GIH][hapmap]
rs6585020	0.90[GIH][hapmap]
rs7081726	0.90[GIH][hapmap]
rs7089193	0.81[EUR][1000 genomes]
rs7089687	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7919142	1.00[JPT][hapmap]
rs7922142	0.81[EUR][1000 genomes]
rs7923004	0.90[GIH][hapmap]

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	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv896003	chr10:112579299-112631211	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv896002	chr10:112579299-112638028	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4917589	TMEM154	trans	cerebellum	SCAN
rs4917589	XPNPEP1	cis	cerebellum	SCAN
rs4917589	HABP2	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112597000-112617200	Weak transcription	Psoas Muscle	Psoas
2	chr10:112597400-112614600	Weak transcription	Aorta	Aorta
3	chr10:112597800-112613400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr10:112597800-112617200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr10:112599600-112613000	Enhancers	Pancreas	Pancrea
6	chr10:112600600-112617200	Weak transcription	Right Ventricle	heart
7	chr10:112600800-112613000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:112602400-112620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr10:112605600-112617000	Weak transcription	Fetal Heart	heart
10	chr10:112607600-112617000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr10:112608200-112616000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr10:112608800-112616000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr10:112608800-112616000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr10:112609000-112615000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr10:112609000-112616000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr10:112609200-112615400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr10:112609200-112616000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr10:112609200-112616000	Enhancers	Placenta	Placenta
19	chr10:112609400-112613000	Enhancers	Fetal Thymus	thymus
20	chr10:112609400-112613800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr10:112609400-112613800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:112609800-112615800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr10:112610000-112613800	Enhancers	HMEC	breast
24	chr10:112610000-112614400	Enhancers	Primary B cells from cord blood	blood
25	chr10:112610400-112613000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:112610600-112613600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr10:112610600-112616000	Enhancers	Fetal Intestine Small	intestine
28	chr10:112610800-112613200	Enhancers	Stomach Mucosa	stomach
29	chr10:112610800-112613800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr10:112611000-112613000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr10:112611000-112613800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:112611000-112614400	Enhancers	Fetal Intestine Large	intestine
33	chr10:112611000-112615800	Enhancers	Primary T cells from cord blood	blood
34	chr10:112611200-112613800	Weak transcription	Fetal Lung	lung
35	chr10:112611200-112616000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:112611200-112616000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr10:112611200-112617200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr10:112611200-112619600	Weak transcription	Osteobl	bone
39	chr10:112611200-112630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:112611400-112613000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr10:112611400-112613600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr10:112611400-112613600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:112611400-112617000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:112611400-112617000	Weak transcription	Adipose Nuclei	Adipose
45	chr10:112611600-112613000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr10:112611600-112613000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr10:112611600-112613200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:112611600-112613200	Enhancers	Liver	Liver
49	chr10:112611600-112613200	Enhancers	Hela-S3	cervix
50	chr10:112611800-112613200	Enhancers	HepG2	liver

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