Variant report

Variant	rs7944346
Chromosome Location	chr11:73244230-73244231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1002126	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1002127	1.00[CEU][hapmap]
rs10501411	0.89[CEU][hapmap]
rs10898925	0.84[AFR][1000 genomes]
rs11235738	1.00[JPT][hapmap]
rs11235745	1.00[JPT][hapmap]
rs11235746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11235759	1.00[JPT][hapmap]
rs11235770	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11235775	1.00[JPT][hapmap]
rs11235809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11820786	0.81[AFR][1000 genomes]
rs11820929	1.00[JPT][hapmap]
rs11821094	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs11823913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11823923	1.00[JPT][hapmap]
rs11824614	1.00[JPT][hapmap]
rs11826896	1.00[CHB][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];0.83[ASN][1000 genomes]
rs12269884	1.00[JPT][hapmap]
rs12274589	1.00[JPT][hapmap]
rs12275766	1.00[JPT][hapmap]
rs12276536	0.86[AFR][1000 genomes]
rs12276892	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]
rs12277924	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282282	1.00[JPT][hapmap]
rs12282790	1.00[JPT][hapmap]
rs12285885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[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]
rs12290701	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12290835	1.00[JPT][hapmap]
rs17132115	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244596	1.00[CEU][hapmap]
rs17244602	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17244616	1.00[CEU][hapmap]
rs17310361	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17310374	1.00[CEU][hapmap]
rs17851510	1.00[CEU][hapmap]
rs1938777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2298469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2298807	1.00[JPT][hapmap]
rs2366780	0.86[AFR][1000 genomes]
rs3825005	1.00[JPT][hapmap]
rs3933402	1.00[JPT][hapmap]
rs56857598	0.82[EUR][1000 genomes]
rs57673166	0.82[EUR][1000 genomes]
rs58573166	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59806295	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60860405	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61516411	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6592521	1.00[JPT][hapmap]
rs7101831	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7102197	1.00[JPT][hapmap]
rs7105681	0.89[CEU][hapmap]
rs7110369	0.89[CEU][hapmap]
rs7114009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs7114376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115055	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7118982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7119167	0.84[AFR][1000 genomes]
rs7122825	0.89[CEU][hapmap]
rs7123985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7129990	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7131383	1.00[JPT][hapmap]
rs7131397	1.00[JPT][hapmap]
rs724111	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7342205	1.00[JPT][hapmap]
rs73544783	0.82[EUR][1000 genomes]
rs7925226	1.00[CEU][hapmap]
rs7927344	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930152	0.82[EUR][1000 genomes]
rs7930454	0.89[CEU][hapmap]
rs7930880	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs7931767	0.82[EUR][1000 genomes]
rs7933355	0.82[EUR][1000 genomes]
rs7934218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935204	0.85[AFR][1000 genomes]
rs7935948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938391	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7944099	1.00[JPT][hapmap]
rs7945825	1.00[CEU][hapmap]
rs7950002	0.81[AFR][1000 genomes]
rs7951072	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7952686	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs876480	1.00[JPT][hapmap]
rs880317	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs947837	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	nsv1048171	chr11:73210060-73271831	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7944346	ARHGEF17	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73232600-73249400	Weak transcription	Brain Germinal Matrix	brain
2	chr11:73239000-73245800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:73240200-73244400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr11:73240200-73245000	Weak transcription	Fetal Kidney	kidney
5	chr11:73240200-73249600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:73240200-73252600	Weak transcription	Placenta	Placenta
7	chr11:73240400-73247800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:73240400-73248600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:73240400-73248600	Weak transcription	Dnd41	blood
10	chr11:73240400-73249200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:73240400-73249400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:73240400-73249400	Weak transcription	HMEC	breast
13	chr11:73240400-73249600	Weak transcription	Adipose Nuclei	Adipose
14	chr11:73240400-73251600	Weak transcription	Fetal Intestine Large	intestine
15	chr11:73240400-73253800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:73240400-73254400	Weak transcription	Stomach Mucosa	stomach
17	chr11:73240600-73249400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr11:73240600-73255400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:73241400-73251400	Weak transcription	Colon Smooth Muscle	Colon
20	chr11:73241600-73247400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr11:73241600-73248800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:73241600-73249400	Weak transcription	Thymus	Thymus
23	chr11:73241600-73250600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:73242000-73245000	Enhancers	Brain Substantia Nigra	brain
25	chr11:73242000-73248000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr11:73242200-73244600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:73242200-73250600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:73242400-73245000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:73242600-73244400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr11:73242600-73249400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr11:73242800-73247800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:73242800-73247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:73242800-73248600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr11:73242800-73248600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr11:73242800-73248800	Weak transcription	GM12878-XiMat	blood
36	chr11:73242800-73249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:73242800-73249400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:73243000-73249400	Weak transcription	Brain Anterior Caudate	brain
39	chr11:73243200-73249400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr11:73243200-73249400	Weak transcription	Right Atrium	heart
41	chr11:73243400-73249400	Weak transcription	Primary T cells from cord blood	blood
42	chr11:73243400-73279600	Weak transcription	Fetal Stomach	stomach
43	chr11:73243800-73244400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:73243800-73245200	Weak transcription	Aorta	Aorta
45	chr11:73243800-73249200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:73243800-73263000	Weak transcription	Fetal Intestine Small	intestine
47	chr11:73244000-73248400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr11:73244000-73248600	Weak transcription	Brain Angular Gyrus	brain
49	chr11:73244000-73248600	Weak transcription	Brain Hippocampus Middle	brain
50	chr11:73244000-73249000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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