Variant report

Variant	rs11939946
Chromosome Location	chr4:175197514-175197515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:175196583..175199350-chr4:175586239..175588239,2	K562	blood:
2	chr4:175179063..175181679-chr4:175196326..175198561,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10520275	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10565	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13128257	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13130276	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17291087	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17291128	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17291408	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41279509	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4287982	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4695915	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4695922	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6553777	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68084371	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824643	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6851312	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72702217	0.86[EUR][1000 genomes]
rs7661236	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7669484	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv881449	chr4:174984230-175225452	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11939946	CEP44	cis	Thyroid	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175154200-175204000	Weak transcription	Aorta	Aorta
2	chr4:175154200-175204200	Weak transcription	Esophagus	oesophagus
3	chr4:175154400-175202400	Weak transcription	Gastric	stomach
4	chr4:175158800-175202000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:175159800-175199800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:175169800-175203600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:175174800-175199800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr4:175174800-175203400	Weak transcription	Thymus	Thymus
9	chr4:175175000-175198600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:175177400-175197800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:175178000-175198600	Weak transcription	K562	blood
12	chr4:175178000-175203600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:175179200-175204000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:175179400-175202400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:175181000-175201600	Weak transcription	Fetal Thymus	thymus
16	chr4:175181600-175203400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:175181600-175203600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:175182200-175202600	Weak transcription	Fetal Intestine Small	intestine
19	chr4:175184200-175197800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:175184200-175199800	Weak transcription	Dnd41	blood
21	chr4:175184200-175202400	Weak transcription	Fetal Intestine Large	intestine
22	chr4:175184200-175203600	Weak transcription	HSMM	muscle
23	chr4:175184400-175200800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr4:175184400-175202400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr4:175184400-175202600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:175184400-175204000	Weak transcription	Left Ventricle	heart
27	chr4:175184800-175202400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:175187400-175198600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:175187600-175198600	Weak transcription	Fetal Brain Female	brain
30	chr4:175187800-175198600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:175187800-175202200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:175188000-175198200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:175188200-175198600	Weak transcription	GM12878-XiMat	blood
34	chr4:175188400-175198000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:175188400-175198600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:175188600-175201800	Weak transcription	Brain Angular Gyrus	brain
37	chr4:175188600-175202600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:175188600-175203400	Weak transcription	Primary B cells from cord blood	blood
39	chr4:175188600-175204000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:175188800-175200400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:175188800-175200600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:175190000-175199200	Weak transcription	Primary T cells from cord blood	blood
43	chr4:175190000-175203400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:175190200-175204000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr4:175190800-175203600	Weak transcription	Fetal Stomach	stomach
46	chr4:175193000-175200000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr4:175193000-175200800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr4:175195400-175201800	Weak transcription	Right Ventricle	heart
49	chr4:175195400-175202600	Weak transcription	Pancreas	Pancrea
50	chr4:175195400-175203800	Weak transcription	Placenta	Placenta

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