Variant report

Variant	rs3740043
Chromosome Location	chr10:91598513-91598514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIF20B-2	chr10:91596975-91600618	ENSG00000232229
2	lnc-KIF20B-2	chr10:91596975-91600618	ENSG00000232229
3	lnc-KIF20B-2	chr10:91596975-91600618	NONHSAT015546
4	lnc-KIF20B-2	chr10:91596975-91599568	NONHSAT015550
5	lnc-KIF20B-2	chr10:91596744-91600600	NONHSAT015553
6	lnc-PANK1-6	chr10:91597369-91599091	NONHSAT015554

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10509581	0.84[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap]
rs10881681	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10881683	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12572608	0.89[GIH][hapmap];1.00[MKK][hapmap]
rs17125834	0.89[GIH][hapmap];1.00[MKK][hapmap]
rs17127001	0.89[GIH][hapmap]
rs1924715	0.83[AFR][1000 genomes]
rs2026554	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34461207	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046241	chr10:91478562-91614437	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh 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
2	nsv869080	chr10:91498641-91712834	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1036581	chr10:91526705-91691536	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1043571	chr10:91568555-92036154	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv551874	chr10:91570211-92036154	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv949678	chr10:91589048-92016474	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3740043	FLJ37201	cis	parietal	SCAN
rs3740043	HECTD2	cis	parietal	SCAN
rs3740043	PCGF5	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91596600-91598600	Active TSS	Brain Anterior Caudate	brain
2	chr10:91596600-91598600	Active TSS	Duodenum Mucosa	Duodenum
3	chr10:91596800-91598800	Active TSS	Fetal Kidney	kidney
4	chr10:91597000-91598800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
5	chr10:91597800-91598600	Enhancers	Stomach Mucosa	stomach
6	chr10:91597800-91599000	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr10:91598000-91598600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr10:91598000-91598600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:91598000-91598600	Flanking Active TSS	Fetal Intestine Large	intestine
10	chr10:91598000-91598600	Flanking Active TSS	Fetal Lung	lung
11	chr10:91598000-91598800	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr10:91598000-91598800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr10:91598000-91598800	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr10:91598200-91598600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr10:91598200-91598600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr10:91598200-91598600	Enhancers	Colon Smooth Muscle	Colon
17	chr10:91598200-91598600	Flanking Active TSS	Fetal Brain Female	brain
18	chr10:91598200-91598600	Flanking Active TSS	Fetal Intestine Small	intestine
19	chr10:91598200-91598600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr10:91598200-91598600	Active TSS	Stomach Smooth Muscle	stomach
21	chr10:91598200-91598800	Enhancers	Primary B cells from peripheral blood	blood
22	chr10:91598200-91598800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr10:91598200-91598800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr10:91598200-91598800	Flanking Active TSS	Fetal Brain Male	brain
25	chr10:91598200-91599000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr10:91598200-91599000	Enhancers	Esophagus	oesophagus
27	chr10:91598200-91604200	Weak transcription	NHEK	skin
28	chr10:91598400-91598600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr10:91598400-91598600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr10:91598400-91598600	Enhancers	Fetal Thymus	thymus
31	chr10:91598400-91598600	Enhancers	Thymus	Thymus
32	chr10:91598400-91598800	Enhancers	Primary T cells from cord blood	blood
33	chr10:91598400-91598800	Active TSS	Primary hematopoietic stem cells	blood
34	chr10:91598400-91598800	Enhancers	Aorta	Aorta
35	chr10:91598400-91598800	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr10:91598400-91599000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
37	chr10:91598400-91599000	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr10:91598400-91599400	Enhancers	Primary B cells from cord blood	blood
39	chr10:91598400-91599400	Enhancers	Fetal Stomach	stomach

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