Variant report

Variant	rs4272809
Chromosome Location	chr11:76172383-76172384
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	chr11:76152066..76158313-chr11:76167740..76173788,10	K562	blood:
2	chr11:76154094..76156954-chr11:76170479..76173196,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158636	Chromatin interaction
ENSG00000255135	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10160382	0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1044265	1.00[ASW][hapmap];0.85[LWK][hapmap];0.82[YRI][hapmap]
rs10793167	0.84[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10793169	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793171	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10899217	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10899219	0.87[AFR][1000 genomes]
rs10899220	0.88[AFR][1000 genomes]
rs10899222	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10899225	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899227	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11236749	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11236752	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11606394	1.00[ASW][hapmap];0.85[LWK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs17749618	0.81[CEU][hapmap]
rs1939467	0.85[CEU][hapmap]
rs1939468	0.81[CEU][hapmap]
rs2251075	0.91[YRI][hapmap]
rs2508738	0.84[AFR][1000 genomes]
rs2508740	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2508741	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2508753	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2508756	1.00[ASW][hapmap];0.85[LWK][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs2508759	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2508760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508761	0.93[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2508762	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2513504	0.96[CEU][hapmap]
rs2513505	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2513508	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2513513	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap]
rs2513515	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs2513520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2513523	0.82[AFR][1000 genomes]
rs2513525	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs3016373	0.87[AFR][1000 genomes]
rs3753051	0.81[CEU][hapmap]
rs3814711	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4245443	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4300410	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625500	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs4945087	0.86[ASW][hapmap];0.83[LWK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs4945090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5023625	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592635	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7106564	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7107058	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7109548	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7123361	0.88[CEU][hapmap]
rs7125552	0.85[CEU][hapmap]
rs7926009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940390	0.84[AFR][1000 genomes]
rs7942257	0.81[CEU][hapmap]
rs7949258	0.85[CEU][hapmap]
rs8848	0.93[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050713	chr11:76147085-76267117	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4272809	ALG8	cis	cerebellum	SCAN
rs4272809	ARHGEF17	cis	cerebellum	SCAN
rs4272809	ARRB1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76157200-76183400	Weak transcription	Gastric	stomach
2	chr11:76157200-76183600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:76157200-76183600	Weak transcription	Spleen	Spleen
4	chr11:76157200-76183800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:76157200-76190200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:76157200-76191200	Weak transcription	Stomach Mucosa	stomach
7	chr11:76157400-76174800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:76157400-76179800	Weak transcription	HSMMtube	muscle
9	chr11:76157400-76183400	Weak transcription	Right Ventricle	heart
10	chr11:76157400-76183600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:76157400-76183600	Weak transcription	Esophagus	oesophagus
12	chr11:76157400-76190200	Weak transcription	Colonic Mucosa	Colon
13	chr11:76157600-76173600	Weak transcription	Brain Substantia Nigra	brain
14	chr11:76157800-76174800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:76158000-76174800	Weak transcription	HMEC	breast
16	chr11:76158000-76177400	Strong transcription	Fetal Thymus	thymus
17	chr11:76158000-76181000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr11:76158200-76179400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:76158200-76190200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:76158600-76172800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr11:76159000-76172800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:76159800-76190400	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:76160000-76178800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:76162200-76173600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:76162200-76183600	Weak transcription	Lung	lung
26	chr11:76164000-76174800	Weak transcription	Brain Germinal Matrix	brain
27	chr11:76164400-76174800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:76164400-76182400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr11:76164400-76183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:76164600-76182800	Weak transcription	Fetal Brain Male	brain
31	chr11:76164800-76188600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:76165600-76173400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr11:76165600-76183400	Weak transcription	Aorta	Aorta
34	chr11:76165600-76183400	Weak transcription	Pancreas	Pancrea
35	chr11:76166000-76173400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:76166000-76175000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr11:76166800-76173000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:76166800-76183600	Weak transcription	Osteobl	bone
39	chr11:76166800-76219400	Weak transcription	Small Intestine	intestine
40	chr11:76167000-76174800	Weak transcription	NHDF-Ad	bronchial
41	chr11:76167000-76176200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr11:76167000-76183800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr11:76167200-76175000	Weak transcription	NH-A	brain
44	chr11:76167200-76190200	Weak transcription	NHLF	lung
45	chr11:76167400-76174800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr11:76167800-76173600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:76167800-76192000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr11:76168200-76174800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:76168200-76179000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:76168400-76174800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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