Variant report

Variant	rs10437720
Chromosome Location	chr11:58883915-58883916
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10128605	0.82[EUR][1000 genomes]
rs10128661	0.85[EUR][1000 genomes]
rs10792219	0.95[CEU][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs10792221	0.93[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896914	0.91[EUR][1000 genomes]
rs10896922	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs10896924	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs10896925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896926	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs10896928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896929	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896930	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896931	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10896932	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896933	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10896934	0.84[EUR][1000 genomes]
rs10896935	0.81[EUR][1000 genomes]
rs10896936	0.90[EUR][1000 genomes]
rs10896937	0.90[EUR][1000 genomes]
rs10896938	0.87[EUR][1000 genomes]
rs10896947	0.89[CEU][hapmap]
rs11229798	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs11229799	0.83[CEU][hapmap];0.93[EUR][1000 genomes]
rs11229800	0.94[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs11229801	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11229837	0.95[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11229840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11229848	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229851	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229852	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229854	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229856	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11823977	0.97[EUR][1000 genomes]
rs11825017	0.97[EUR][1000 genomes]
rs12271831	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12272113	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12274008	0.92[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12275487	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12278163	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12280068	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12283633	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12292185	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12293649	0.92[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12293695	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12362905	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12802129	0.97[EUR][1000 genomes]
rs17153379	0.97[EUR][1000 genomes]
rs17153383	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17153415	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938588	0.97[EUR][1000 genomes]
rs1938589	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1938781	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2096544	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2096586	0.85[EUR][1000 genomes]
rs2096587	0.88[EUR][1000 genomes]
rs2105506	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2105507	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2154628	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2186380	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2282482	0.95[EUR][1000 genomes]
rs2282483	0.94[EUR][1000 genomes]
rs2839968	0.89[CEU][hapmap]
rs2849739	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34027305	0.91[EUR][1000 genomes]
rs34239454	0.93[EUR][1000 genomes]
rs34501069	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35293773	0.93[EUR][1000 genomes]
rs3802961	0.97[EUR][1000 genomes]
rs474847	0.92[EUR][1000 genomes]
rs55657403	0.84[EUR][1000 genomes]
rs55689653	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55989038	0.83[EUR][1000 genomes]
rs56137001	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56239606	0.84[EUR][1000 genomes]
rs58722008	0.86[EUR][1000 genomes]
rs61902181	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61902223	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7126078	0.97[EUR][1000 genomes]
rs7933787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7950880	0.85[AMR][1000 genomes];0.94[EUR][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	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv469559	chr11:58730785-58887639	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv482906	chr11:58730785-58887639	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv471671	chr11:58730786-58887639	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv2757447	chr11:58746238-58906018	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv975329	chr11:58767290-58907813	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv430388	chr11:58769524-58925824	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
11	nsv468578	chr11:58790628-58901763	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv555147	chr11:58790628-58901763	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10437720	CD5	cis	cerebellum	SCAN
rs10437720	C11orf31	cis	parietal	SCAN
rs10437720	OR1S2	cis	parietal	SCAN
rs10437720	FAM111A	cis	parietal	SCAN
rs10437720	OR5AK2	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58875200-58909600	Weak transcription	Stomach Mucosa	stomach
2	chr11:58875400-58884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:58875400-58884000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:58875400-58884000	Weak transcription	Esophagus	oesophagus
5	chr11:58875400-58885000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:58875400-58909600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:58876000-58884000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:58876000-58884200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:58876000-58884400	Weak transcription	Fetal Brain Female	brain
10	chr11:58876000-58884600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:58876000-58885000	Weak transcription	Fetal Intestine Large	intestine
12	chr11:58876000-58886400	Weak transcription	HSMM	muscle
13	chr11:58876000-58888000	Weak transcription	Fetal Kidney	kidney
14	chr11:58876200-58884000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:58876200-58884200	Weak transcription	A549	lung
16	chr11:58876200-58884600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:58876200-58885000	Weak transcription	HepG2	liver
18	chr11:58876200-58885600	Weak transcription	HUVEC	blood vessel
19	chr11:58876200-58891800	Weak transcription	Fetal Heart	heart
20	chr11:58876200-58892000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:58876600-58884000	Strong transcription	Fetal Thymus	thymus
22	chr11:58876600-58884400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:58876600-58884600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr11:58876600-58884600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr11:58876600-58885400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr11:58877000-58884000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:58878400-58884600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:58879600-58884400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr11:58879800-58885000	Weak transcription	NHDF-Ad	bronchial
30	chr11:58879800-58885000	Weak transcription	NHLF	lung
31	chr11:58880400-58887000	ZNF genes & repeats	GM12878-XiMat	blood
32	chr11:58880600-58884400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:58880600-58884600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:58880800-58884000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:58880800-58884000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr11:58880800-58884000	Strong transcription	Fetal Muscle Leg	muscle
37	chr11:58880800-58884000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr11:58880800-58884200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr11:58880800-58884400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr11:58880800-58885400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:58880800-58894800	ZNF genes & repeats	Dnd41	blood
42	chr11:58881400-58884000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr11:58881600-58884000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:58881600-58884800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:58881600-58884800	Weak transcription	NHEK	skin
46	chr11:58881600-58903600	Weak transcription	Hela-S3	cervix
47	chr11:58882200-58885000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:58882400-58884600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr11:58882400-58885000	Weak transcription	HMEC	breast
50	chr11:58882600-58884000	Weak transcription	Primary hematopoietic stem cells	blood

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