Variant report

Variant	rs13006863
Chromosome Location	chr2:74463566-74463567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74447215..74450146-chr2:74463449..74465120,2	K562	blood:
2	chr2:74457826..74461318-chr2:74461527..74466761,7	K562	blood:
3	chr2:74424696..74427673-chr2:74460558..74464630,6	MCF-7	breast:
4	chr2:74447215..74450146-chr2:74463449..74466578,3	K562	blood:
5	chr2:74457826..74461075-chr2:74461527..74464148,4	K562	blood:

Variant related genes	Relation type
ENSG00000065911	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10186159	0.94[ASN][1000 genomes]
rs12053233	0.91[CEU][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13034587	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34481365	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4853018	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7579359	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7587117	0.89[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.85[LWK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][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	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
2	nsv834261	chr2:74391709-74613720	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3401140	chr2:74439333-74533696	Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv3380034	chr2:74439354-74533666	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Post-traumatic stress disorder (asjusted for relatedness)	23726511	GWAS catalog
Immune reponse to smallpox (secreted TNF-alpha)	22610502	GWAS catalog

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74427400-74484400	Weak transcription	Fetal Lung	lung
2	chr2:74427800-74494200	Weak transcription	Brain Germinal Matrix	brain
3	chr2:74439800-74525200	Weak transcription	Fetal Brain Male	brain
4	chr2:74441800-74466000	Weak transcription	Adipose Nuclei	Adipose
5	chr2:74441800-74490400	Weak transcription	Fetal Brain Female	brain
6	chr2:74442400-74477400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:74442800-74465200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr2:74444800-74494200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:74448800-74494000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:74449200-74465200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:74449200-74470600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:74449200-74502200	Weak transcription	Spleen	Spleen
13	chr2:74449400-74494000	Weak transcription	Primary T cells from cord blood	blood
14	chr2:74449400-74507000	Weak transcription	Brain Anterior Caudate	brain
15	chr2:74450000-74494000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr2:74453800-74465800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:74454200-74508200	Weak transcription	Ovary	ovary
18	chr2:74454400-74466200	Weak transcription	Esophagus	oesophagus
19	chr2:74454400-74470200	Weak transcription	Gastric	stomach
20	chr2:74454400-74471800	Weak transcription	Psoas Muscle	Psoas
21	chr2:74454400-74474200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:74455400-74464800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:74455400-74469600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:74455400-74469800	Weak transcription	Left Ventricle	heart
25	chr2:74455400-74470200	Weak transcription	Right Ventricle	heart
26	chr2:74455400-74473600	Weak transcription	Lung	lung
27	chr2:74455600-74480000	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:74458600-74483400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:74458800-74488200	Weak transcription	Pancreas	Pancrea
30	chr2:74461800-74474000	Weak transcription	Fetal Stomach	stomach
31	chr2:74462200-74494000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:74462400-74493800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:74462600-74473600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:74462600-74509600	Weak transcription	Brain Substantia Nigra	brain
35	chr2:74462800-74467000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:74462800-74469600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:74462800-74473200	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:74462800-74473400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:74463000-74544800	Weak transcription	Brain Angular Gyrus	brain
40	chr2:74463400-74473000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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