Variant report

Variant	rs2279865
Chromosome Location	chr11:66203025-66203026
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66197807..66202007-chr11:66202412..66207271,7	K562	blood:
2	chr11:66187993..66190570-chr11:66199449..66203707,3	K562	blood:
3	chr11:66184274..66187220-chr11:66201977..66203892,2	K562	blood:
4	chr11:66188562..66190830-chr11:66202207..66204001,2	K562	blood:
5	chr11:66202690..66204715-chr11:66204963..66207205,2	MCF-7	breast:
6	chr11:66200896..66204077-chr11:66204378..66206381,3	K562	blood:

Variant related genes	Relation type
ENSG00000174547	Chromatin interaction
ENSG00000201733	Chromatin interaction
ENSG00000174576	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10501397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10896124	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10896125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10896129	0.84[EUR][1000 genomes]
rs11227495	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11227497	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11227498	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11227499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11227500	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11227501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11227502	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11227503	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11227509	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11227510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11227511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11227512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11227514	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11227515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11227523	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11227525	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11227527	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11227534	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs11550299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11821155	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11822028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11822099	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11824771	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12099041	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12221821	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12272545	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17065	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17147644	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17495838	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs17496250	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17496586	0.82[EUR][1000 genomes]
rs17580784	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1785640	0.83[YRI][hapmap]
rs2075792	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs2276406	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277302	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279864	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2298806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305534	0.84[EUR][1000 genomes]
rs2305535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28414721	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3179961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35733139	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3737525	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs3741360	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3816492	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs3819247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3825065	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3867131	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3892818	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4542420	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4576	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4630309	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4930182	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4930183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930377	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4930378	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930380	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56144989	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57045447	0.84[EUR][1000 genomes]
rs57207756	0.85[EUR][1000 genomes]
rs57288351	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57596493	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57634456	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57691879	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57724777	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59829960	0.84[EUR][1000 genomes]
rs59982644	0.85[EUR][1000 genomes]
rs60358007	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60645853	0.85[EUR][1000 genomes]
rs61561111	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61582507	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7104378	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7116921	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7116940	0.84[EUR][1000 genomes]
rs7123176	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7928882	1.00[GIH][hapmap];0.86[MEX][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7939759	0.84[EUR][1000 genomes]
rs7943327	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7950407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7950790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[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	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
2	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
3	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
6	nsv897786	chr11:66203025-66244015	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2279865	DPP3	cis	Thyroid	GTEx
rs2279865	CTD-3074O7.5	cis	Esophagus Mucosa	GTEx
rs2279865	CTD-3074O7.5	cis	Whole Blood	GTEx
rs2279865	RBM4	cis	cerebellum	SCAN
rs2279865	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs2279865	C11orf80	cis	cerebellum	SCAN
rs2279865	CHKA	cis	cerebellum	SCAN
rs2279865	ASRGL1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66188800-66205600	Weak transcription	Right Atrium	heart
2	chr11:66189000-66204800	Weak transcription	Fetal Heart	heart
3	chr11:66189200-66205600	Weak transcription	Stomach Mucosa	stomach
4	chr11:66190200-66205000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:66191400-66203600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:66191600-66205600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:66192200-66204400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:66197200-66204400	Weak transcription	Fetal Brain Male	brain
9	chr11:66197400-66203200	Weak transcription	Colonic Mucosa	Colon
10	chr11:66197600-66203200	Weak transcription	HepG2	liver
11	chr11:66197600-66203400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:66197600-66205600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:66198600-66205400	Weak transcription	Small Intestine	intestine
14	chr11:66199000-66203400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:66199200-66205000	Strong transcription	Fetal Stomach	stomach
16	chr11:66199400-66205000	Strong transcription	Fetal Intestine Small	intestine
17	chr11:66200000-66204600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:66200000-66204800	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr11:66200200-66204800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:66200200-66204800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr11:66200600-66204200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:66200800-66204800	Weak transcription	GM12878-XiMat	blood
23	chr11:66201000-66203200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr11:66201000-66204400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:66201000-66205400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr11:66201000-66205400	Weak transcription	HSMM	muscle
27	chr11:66201200-66204800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:66201200-66205400	Weak transcription	Psoas Muscle	Psoas
29	chr11:66201800-66204400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:66201800-66204600	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr11:66201800-66204600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr11:66201800-66205000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr11:66201800-66205400	Weak transcription	HMEC	breast
34	chr11:66202000-66204600	Strong transcription	Liver	Liver
35	chr11:66202200-66204600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:66202200-66204800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:66202200-66204800	Strong transcription	Fetal Intestine Large	intestine
38	chr11:66202400-66203200	Strong transcription	Primary B cells from cord blood	blood
39	chr11:66202400-66203600	Strong transcription	Brain Angular Gyrus	brain
40	chr11:66202400-66204000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:66202400-66204000	Strong transcription	Fetal Brain Female	brain
42	chr11:66202400-66204200	Strong transcription	HUVEC	blood vessel
43	chr11:66202400-66204400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:66202400-66204600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:66202400-66204600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:66202400-66204600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:66202400-66204600	Strong transcription	Colon Smooth Muscle	Colon
48	chr11:66202400-66204600	Strong transcription	Fetal Thymus	thymus
49	chr11:66202400-66204600	Strong transcription	Hela-S3	cervix
50	chr11:66202400-66204600	Strong transcription	Monocytes-CD14+_RO01746	blood

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