Variant report

Variant	rs12276892
Chromosome Location	chr11:73283990-73283991
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1002126	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1002127	1.00[CEU][hapmap]
rs10501411	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11235738	1.00[JPT][hapmap]
rs11235745	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11235746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11235759	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11235770	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs11235775	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11235809	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11823913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11826896	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11826909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11828904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12269884	1.00[JPT][hapmap]
rs12274589	1.00[JPT][hapmap]
rs12277924	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12282790	1.00[JPT][hapmap]
rs12285885	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12288753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12290623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs12290701	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12290835	1.00[JPT][hapmap]
rs17132115	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17244596	1.00[CEU][hapmap]
rs17244602	1.00[CEU][hapmap]
rs17244616	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17310361	1.00[CEU][hapmap]
rs17310374	1.00[CEU][hapmap]
rs17851510	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap]
rs1938777	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs2298469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3825005	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs57491850	0.82[EUR][1000 genomes]
rs58573166	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59806295	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60860405	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61516411	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7101831	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7110369	0.89[CEU][hapmap]
rs7114009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7114376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7115055	1.00[CEU][hapmap]
rs7118982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7123985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7125598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.88[ASN][1000 genomes]
rs7129990	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs7131397	1.00[JPT][hapmap]
rs724111	1.00[CEU][hapmap]
rs73548693	0.82[EUR][1000 genomes]
rs73550316	0.82[EUR][1000 genomes]
rs7925226	1.00[CEU][hapmap]
rs7927344	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7930454	0.89[CEU][hapmap]
rs7934218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7935948	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7938391	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7941359	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7944346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7945825	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7951072	1.00[CEU][hapmap]
rs7952686	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs876480	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs880317	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9888218	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv983188	chr11:73273934-73307064	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12276892	ARHGEF17	cis	multi-tissue	Pritchard
rs12276892	CCND1	cis	cerebellum	SCAN
rs12276892	ARHGEF17	cis	Whole Blood	GTEx
rs12276892	P2RY2	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73250000-73307800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr11:73251000-73288800	Weak transcription	Thymus	Thymus
3	chr11:73253800-73307000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:73263200-73306000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:73263800-73288800	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:73264600-73287000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:73265400-73287200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:73266600-73307800	Weak transcription	Fetal Intestine Small	intestine
9	chr11:73267400-73284800	Weak transcription	Right Atrium	heart
10	chr11:73270600-73288000	Weak transcription	NHLF	lung
11	chr11:73272200-73307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:73274600-73287000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:73274600-73287000	Weak transcription	Brain Substantia Nigra	brain
14	chr11:73274800-73290800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr11:73275200-73286800	Weak transcription	Brain Anterior Caudate	brain
16	chr11:73275200-73287000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:73275400-73284600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:73275400-73288800	Weak transcription	GM12878-XiMat	blood
19	chr11:73275400-73307000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:73276200-73287200	Weak transcription	Brain Angular Gyrus	brain
21	chr11:73276400-73287400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:73276400-73289800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:73276400-73296800	Weak transcription	Fetal Muscle Leg	muscle
24	chr11:73276400-73299200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr11:73276400-73307000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:73276600-73286800	Weak transcription	Fetal Brain Female	brain
27	chr11:73277200-73285800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:73277200-73299600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr11:73277400-73307800	Weak transcription	Fetal Intestine Large	intestine
30	chr11:73277600-73286800	Weak transcription	Brain Germinal Matrix	brain
31	chr11:73277600-73287200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr11:73277600-73293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:73278000-73288000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:73278200-73284000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:73278200-73284000	Weak transcription	Left Ventricle	heart
36	chr11:73278200-73289000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:73278400-73286800	Weak transcription	Brain Hippocampus Middle	brain
38	chr11:73278600-73284000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:73278600-73287400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:73278800-73284000	Weak transcription	K562	blood
41	chr11:73279200-73288800	Weak transcription	Fetal Thymus	thymus
42	chr11:73279400-73289200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr11:73279400-73307000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr11:73279600-73291200	Weak transcription	Ovary	ovary
45	chr11:73279800-73284800	Weak transcription	Psoas Muscle	Psoas
46	chr11:73280000-73289800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr11:73280000-73299400	Weak transcription	Fetal Stomach	stomach
48	chr11:73280200-73289000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr11:73280400-73284000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:73280600-73284000	Weak transcription	Dnd41	blood

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