Variant report

Variant	rs17244616
Chromosome Location	chr11:73293112-73293113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1002127	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10501411	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10751226	1.00[CHB][hapmap]
rs11235770	1.00[CEU][hapmap]
rs11235809	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11820577	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11822984	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11823913	1.00[CEU][hapmap]
rs11828904	1.00[CEU][hapmap]
rs12276892	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12285885	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12288753	1.00[CEU][hapmap]
rs12290623	1.00[CEU][hapmap]
rs12290785	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs17244602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17310361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17310374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17851510	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1938777	1.00[CEU][hapmap]
rs2298469	1.00[CEU][hapmap]
rs56742470	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56857598	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56884659	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57491850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57673166	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58334887	1.00[ASN][1000 genomes]
rs58564192	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59806295	0.83[EUR][1000 genomes]
rs61516411	0.83[EUR][1000 genomes]
rs6592526	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101561	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110369	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs7114009	1.00[CEU][hapmap]
rs7114376	1.00[CEU][hapmap]
rs7115055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118057	0.91[AFR][1000 genomes]
rs7118982	1.00[CEU][hapmap]
rs7123985	1.00[CEU][hapmap]
rs7125598	1.00[CEU][hapmap]
rs7129546	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129990	0.89[CEU][hapmap]
rs724111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73543000	1.00[ASN][1000 genomes]
rs73544710	1.00[ASN][1000 genomes]
rs73544711	1.00[ASN][1000 genomes]
rs73544716	1.00[ASN][1000 genomes]
rs73544720	1.00[ASN][1000 genomes]
rs73544729	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73544767	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73544783	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546720	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546735	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548680	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548688	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73550316	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs7930152	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930907	0.84[AFR][1000 genomes]
rs7931767	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933355	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934218	1.00[CEU][hapmap]
rs7935948	1.00[CEU][hapmap]
rs7938391	1.00[CEU][hapmap]
rs7941359	1.00[CEU][hapmap]
rs7943721	0.91[AFR][1000 genomes]
rs7944346	1.00[CEU][hapmap]
rs7945825	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950375	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv975202	chr11:73289057-73294849	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking 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
rs17244616	ARHGEF17	cis	Whole Blood	GTEx
rs17244616	CCND1	cis	cerebellum	SCAN
rs17244616	RELT	cis	lymphoblastoid	seeQTL
rs17244616	P2RY2	cis	cerebellum	SCAN

Chromatin state (count:75 , 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	chr11:73253800-73307000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:73263200-73306000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:73266600-73307800	Weak transcription	Fetal Intestine Small	intestine
5	chr11:73272200-73307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:73275400-73307000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr11:73276400-73296800	Weak transcription	Fetal Muscle Leg	muscle
8	chr11:73276400-73299200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr11:73276400-73307000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:73277200-73299600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr11:73277400-73307800	Weak transcription	Fetal Intestine Large	intestine
12	chr11:73277600-73293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:73279400-73307000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:73280000-73299400	Weak transcription	Fetal Stomach	stomach
15	chr11:73280600-73296200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:73281600-73307800	Weak transcription	Hela-S3	cervix
17	chr11:73281800-73295400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:73282000-73296800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:73282200-73296400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:73282200-73296600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:73282200-73297000	Weak transcription	HMEC	breast
22	chr11:73282200-73297200	Weak transcription	NH-A	brain
23	chr11:73282400-73293800	Weak transcription	HSMM	muscle
24	chr11:73285200-73294600	Weak transcription	Right Ventricle	heart
25	chr11:73285200-73303600	Weak transcription	Left Ventricle	heart
26	chr11:73285200-73306600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:73286000-73294800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr11:73286200-73295000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr11:73286800-73307600	Weak transcription	Lung	lung
30	chr11:73287800-73306200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:73288000-73306200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:73288200-73293800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:73288400-73307800	Weak transcription	Aorta	Aorta
34	chr11:73288800-73307600	Weak transcription	Fetal Kidney	kidney
35	chr11:73289000-73304800	Weak transcription	Thymus	Thymus
36	chr11:73289000-73305800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr11:73289200-73293800	Weak transcription	Psoas Muscle	Psoas
38	chr11:73289200-73294400	Weak transcription	Brain Substantia Nigra	brain
39	chr11:73289200-73299400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr11:73289200-73300800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:73289200-73304600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr11:73289200-73304800	Weak transcription	Dnd41	blood
43	chr11:73289400-73293800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:73289400-73293800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr11:73289400-73297400	Weak transcription	Spleen	Spleen
46	chr11:73289400-73299400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr11:73289400-73304400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:73289400-73307000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr11:73289600-73306800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:73290000-73297200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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