Variant report

Variant	rs10799541
Chromosome Location	chr1:224411596-224411597
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224406207..224408760-chr1:224411418..224413367,2	K562	blood:
2	chr1:224369856..224371888-chr1:224410575..224412569,2	K562	blood:
3	chr1:224410677..224413155-chr1:224413701..224415369,2	MCF-7	breast:
4	chr1:224410361..224412569-chr1:224413431..224415839,2	K562	blood:

Variant related genes	Relation type
ENSG00000237101	Chromatin interaction
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1060394	0.90[CHB][hapmap]
rs10799545	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916488	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11589025	0.82[CHB][hapmap];0.83[GIH][hapmap]
rs12022755	0.83[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap]
rs12081432	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1807899	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976786	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34011742	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61826430	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10799541	DEGS1	cis	cerebellum	SCAN
rs10799541	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs10799541	FBXO28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224393800-224414200	Weak transcription	Colonic Mucosa	Colon
3	chr1:224394000-224414000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:224394000-224414600	Weak transcription	HMEC	breast
5	chr1:224398000-224414200	Weak transcription	Spleen	Spleen
6	chr1:224399400-224414200	Weak transcription	Adipose Nuclei	Adipose
7	chr1:224399400-224414200	Weak transcription	Brain Anterior Caudate	brain
8	chr1:224401400-224413800	Weak transcription	Primary B cells from cord blood	blood
9	chr1:224401400-224413800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:224401400-224414800	Weak transcription	Right Ventricle	heart
11	chr1:224401600-224414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:224401800-224415200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:224401800-224427600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:224401800-224475400	Weak transcription	Esophagus	oesophagus
15	chr1:224402200-224413800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:224402200-224414200	Weak transcription	GM12878-XiMat	blood
17	chr1:224404000-224411600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:224406000-224414200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:224406200-224413800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:224406200-224414200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:224406200-224414200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:224406200-224414200	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:224406200-224414400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:224406400-224414200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr1:224406800-224414400	Weak transcription	Pancreas	Pancrea
29	chr1:224407200-224411600	Weak transcription	K562	blood
30	chr1:224407200-224413800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:224407200-224414400	Weak transcription	Placenta	Placenta
32	chr1:224407600-224411800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:224407600-224411800	Weak transcription	HepG2	liver
34	chr1:224407600-224414200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:224407600-224414200	Weak transcription	Fetal Thymus	thymus
36	chr1:224407600-224414200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:224407600-224434000	Weak transcription	Fetal Brain Male	brain
38	chr1:224407800-224414200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:224407800-224414200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:224407800-224414200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:224408000-224414200	Weak transcription	Gastric	stomach
42	chr1:224410000-224412200	Enhancers	Stomach Mucosa	stomach
43	chr1:224410400-224414200	Weak transcription	Liver	Liver
44	chr1:224411000-224411600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:224411000-224411600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:224411000-224411600	Enhancers	Left Ventricle	heart
47	chr1:224411000-224411600	Enhancers	Psoas Muscle	Psoas
48	chr1:224411000-224411800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:224411000-224412000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr1:224411000-224412200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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