Variant report

Variant	rs16823598
Chromosome Location	chr2:144990823-144990824
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:144989299..144991391-chr2:144999087..145001550,2	K562	blood:
2	chr2:144988081..144991559-chr2:144993031..144996517,4	K562	blood:
3	chr2:144984323..144985940-chr2:144989560..144991924,2	K562	blood:

Variant related genes	Relation type
ENSG00000121964	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16823571	0.81[LWK][hapmap];0.90[MKK][hapmap];1.00[AMR][1000 genomes]
rs16823579	0.81[LWK][hapmap];0.93[MKK][hapmap]
rs16823594	1.00[LWK][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16823596	1.00[LWK][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs16823607	1.00[AMR][1000 genomes]
rs16823609	1.00[MKK][hapmap]
rs16823684	1.00[AMR][1000 genomes]
rs16823718	1.00[AMR][1000 genomes]
rs60695751	1.00[AMR][1000 genomes]
rs6761553	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72992123	1.00[AMR][1000 genomes]
rs72992134	1.00[AMR][1000 genomes]
rs72992136	1.00[AMR][1000 genomes]
rs72992138	1.00[AMR][1000 genomes]
rs73008262	1.00[AMR][1000 genomes]
rs73008283	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532755	chr2:144631279-145270874	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1006344	chr2:144657716-145334899	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535951	chr2:144657716-145334899	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1067624	chr2:144657717-145425705	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv531413	chr2:144657717-145425705	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv532756	chr2:144746353-145315596	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1008032	chr2:144840552-145234229	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv834396	chr2:144842187-145019465	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv997624	chr2:144906679-145294503	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv535952	chr2:144906679-145294503	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
11	nsv532757	chr2:144922143-145263446	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv916172	chr2:144970681-145425713	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16823598	LOC96610	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:144962600-144998600	Weak transcription	Psoas Muscle	Psoas
2	chr2:144964400-144998200	Weak transcription	Fetal Kidney	kidney
3	chr2:144965400-145010000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:144965600-144992400	Weak transcription	Fetal Stomach	stomach
5	chr2:144974000-144995200	Weak transcription	Primary B cells from cord blood	blood
6	chr2:144977400-144995200	Weak transcription	Left Ventricle	heart
7	chr2:144978400-144991000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:144978400-144991200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:144984000-144994600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:144985400-144998400	Weak transcription	Small Intestine	intestine
11	chr2:144987000-144992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:144987400-144991800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:144987400-144992200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:144988000-144991200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:144988200-144991800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:144988200-144998600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:144988400-144991000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr2:144988400-144991000	Weak transcription	Brain Germinal Matrix	brain
19	chr2:144988400-144991000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:144988400-144995200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:144988600-144991000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:144988600-144991800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:144988800-144991400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:144988800-144992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:144988800-144998000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:144989000-144992200	Enhancers	Fetal Brain Male	brain
27	chr2:144989200-144992000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:144989400-144993200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:144989600-144992400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:144989800-144991000	Weak transcription	Fetal Lung	lung
31	chr2:144989800-144991200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:144989800-144991800	Enhancers	K562	blood
33	chr2:144990000-144991000	Weak transcription	Fetal Brain Female	brain
34	chr2:144990000-144991400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:144990000-144991800	Enhancers	GM12878-XiMat	blood
36	chr2:144990000-144992000	Enhancers	Primary hematopoietic stem cells	blood
37	chr2:144990200-144991800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:144990200-144992800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:144990400-144991000	Enhancers	Brain Hippocampus Middle	brain
40	chr2:144990400-144991400	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr2:144990400-144991400	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr2:144990400-144991800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr2:144990400-144992400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr2:144990400-144992800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:144990400-144992800	Enhancers	Brain Substantia Nigra	brain
46	chr2:144990400-144993000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr2:144990600-144991200	Enhancers	Adipose Nuclei	Adipose
48	chr2:144990600-144992000	Enhancers	Brain Cingulate Gyrus	brain
49	chr2:144990600-144992800	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr2:144990800-144991000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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