Variant report

Variant	rs27499
Chromosome Location	chr5:115636976-115636977
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	chr5:115632385..115634405-chr5:115635053..115637473,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10042163	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs10055039	1.00[ASW][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap]
rs10478283	0.92[MEX][hapmap]
rs1090076	1.00[JPT][hapmap]
rs11241386	0.81[ASN][1000 genomes]
rs11957456	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs12055304	0.86[MEX][hapmap]
rs12653124	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[YRI][hapmap]
rs1351136	0.81[ASN][1000 genomes]
rs1351137	0.81[ASN][1000 genomes]
rs1396480	1.00[YRI][hapmap]
rs1508874	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs153578	0.86[ASN][1000 genomes]
rs153591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153592	0.86[ASN][1000 genomes]
rs153612	0.84[ASN][1000 genomes]
rs153614	0.90[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs168833	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs187591	0.83[ASN][1000 genomes]
rs194182	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs2136206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs253953	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs253956	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs253960	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs253967	0.83[EUR][1000 genomes]
rs254149	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs254154	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27500	0.81[ASN][1000 genomes]
rs28083	0.86[ASN][1000 genomes]
rs28125	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs37182	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs37183	0.90[CHD][hapmap]
rs4463206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4920906	1.00[ASW][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap]
rs6594950	0.80[MEX][hapmap]
rs6594954	0.93[MEX][hapmap]
rs6594955	1.00[YRI][hapmap]
rs6860795	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap]
rs6877029	0.93[MEX][hapmap]
rs6878279	1.00[YRI][hapmap]
rs6896229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs712575	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs712580	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs712581	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72808983	0.82[ASN][1000 genomes]
rs7704903	0.86[MEX][hapmap]
rs784482	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785368	0.90[CEU][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs804141	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs804142	0.81[ASN][1000 genomes]
rs9285884	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap]
rs9326992	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv882746	chr5:115566026-115704566	Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv882747	chr5:115566636-115662510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv882748	chr5:115584159-115669950	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv869754	chr5:115634234-115696094	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs27499	DMXL1	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115613400-115641600	Weak transcription	HSMM	muscle
2	chr5:115625600-115639200	Weak transcription	Fetal Stomach	stomach
3	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:115626600-115641600	Weak transcription	Fetal Brain Male	brain
5	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:115627800-115639200	Weak transcription	Placenta	Placenta
7	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:115628400-115639200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:115628400-115641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:115628600-115639400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel
13	chr5:115629400-115638200	Weak transcription	Pancreas	Pancrea
14	chr5:115629400-115638400	Weak transcription	Right Ventricle	heart
15	chr5:115631400-115637800	Weak transcription	Fetal Thymus	thymus
16	chr5:115631800-115640600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:115631800-115641800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:115632000-115639200	Weak transcription	Lung	lung
19	chr5:115632000-115643000	Weak transcription	NH-A	brain
20	chr5:115632600-115640400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:115632600-115640600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:115632600-115643400	Weak transcription	Stomach Mucosa	stomach
23	chr5:115632800-115639600	Weak transcription	Brain Angular Gyrus	brain
24	chr5:115632800-115642600	Weak transcription	NHDF-Ad	bronchial
25	chr5:115633200-115640800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:115633600-115639800	Weak transcription	Spleen	Spleen
27	chr5:115633800-115637600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:115633800-115638200	Weak transcription	HSMMtube	muscle
29	chr5:115633800-115640400	Weak transcription	Esophagus	oesophagus
30	chr5:115634000-115637800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:115634000-115640400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr5:115634200-115637400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:115634200-115637600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:115634200-115637600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:115634200-115639000	Weak transcription	Small Intestine	intestine
36	chr5:115634200-115639200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:115634200-115639200	Weak transcription	Colonic Mucosa	Colon
38	chr5:115634200-115639200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr5:115634200-115639400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:115634200-115639400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:115634200-115639600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:115634200-115639600	Weak transcription	Dnd41	blood
43	chr5:115634200-115640200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:115634200-115640400	Weak transcription	Fetal Intestine Small	intestine
45	chr5:115634200-115640600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:115634200-115640600	Weak transcription	Thymus	Thymus
47	chr5:115634200-115640800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr5:115634200-115640800	Weak transcription	Psoas Muscle	Psoas
49	chr5:115634200-115641400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr5:115634200-115641800	Weak transcription	Brain Inferior Temporal Lobe	brain

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