Variant report

Variant	rs2044099
Chromosome Location	chr15:78332022-78332023
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	chr15:78331100..78333926-chr15:78382964..78385819,2	K562	blood:

Variant related genes	Relation type
ENSG00000199633	Chromatin interaction
ENSG00000183476	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1004855	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs10444863	0.84[CEU][hapmap]
rs10519181	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072716	0.91[CHB][hapmap]
rs11631578	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs11634607	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs11638311	0.91[ASN][1000 genomes]
rs11852768	0.81[ASN][1000 genomes]
rs12148365	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12442213	0.83[CHB][hapmap]
rs12591418	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12593545	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs12594823	0.89[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs12899061	0.83[ASN][1000 genomes]
rs12901812	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs12907814	0.81[ASN][1000 genomes]
rs12911332	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs12916362	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1348257	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1442293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16969422	0.84[CEU][hapmap]
rs1837913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1992470	0.90[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2028546	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2241885	0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs2867985	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2903702	0.81[ASN][1000 genomes]
rs3803380	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4395040	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4886553	1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4886554	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4886555	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886989	0.84[CEU][hapmap]
rs4886992	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs4886994	0.93[ASN][1000 genomes]
rs4886995	0.83[CHB][hapmap]
rs4886996	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4886999	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4887000	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs55704745	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56317829	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57220134	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58578288	0.84[ASN][1000 genomes]
rs62011511	0.84[ASN][1000 genomes]
rs7166819	0.81[ASN][1000 genomes]
rs7170746	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs7173128	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs7174489	0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs7181594	0.82[ASN][1000 genomes]
rs72732535	0.82[EUR][1000 genomes]
rs8030713	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8030873	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs872926	0.84[CEU][hapmap]
rs894301	0.84[CEU][hapmap]
rs9047	0.83[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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2044099	CCDC33	cis	cerebellum	SCAN
rs2044099	CLK3	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78301400-78342200	Weak transcription	HMEC	breast
3	chr15:78303200-78342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:78307200-78342000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:78316000-78332400	Weak transcription	Hela-S3	cervix
7	chr15:78317000-78344400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:78317400-78342600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:78317800-78344400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:78317800-78344400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:78320200-78334400	Weak transcription	Aorta	Aorta
12	chr15:78321200-78343800	Weak transcription	NHEK	skin
13	chr15:78322200-78336600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:78322200-78341000	Weak transcription	Brain Germinal Matrix	brain
15	chr15:78322400-78336600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:78324000-78332200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr15:78324600-78334400	Weak transcription	Ovary	ovary
18	chr15:78325600-78337800	Genic enhancers	Fetal Thymus	thymus
19	chr15:78325800-78333600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr15:78326200-78332800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:78327400-78339600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:78327600-78333600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr15:78327600-78351400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr15:78327800-78342000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr15:78328000-78332200	Enhancers	Small Intestine	intestine
26	chr15:78328000-78334600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:78328000-78335400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:78328000-78336600	Weak transcription	Fetal Brain Female	brain
29	chr15:78328000-78336800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:78328000-78341800	Weak transcription	Fetal Brain Male	brain
31	chr15:78328200-78334200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:78328400-78332200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:78328400-78332200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr15:78328400-78332400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr15:78328400-78333000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:78328400-78333400	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr15:78328400-78333800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr15:78328400-78334000	Weak transcription	Osteobl	bone
39	chr15:78328400-78334200	Weak transcription	NHLF	lung
40	chr15:78328400-78334800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:78328400-78339000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:78328400-78342200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:78328600-78332400	Weak transcription	NHDF-Ad	bronchial
44	chr15:78328600-78333200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr15:78328600-78333200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:78328600-78334200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:78328600-78334600	Weak transcription	Fetal Kidney	kidney
48	chr15:78328600-78336400	Weak transcription	NH-A	brain
49	chr15:78328600-78342200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:78328800-78332600	Strong transcription	Stomach Smooth Muscle	stomach

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