Variant report

Variant	rs12099129
Chromosome Location	chr11:73091318-73091319
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:73090804..73093767-chr11:73094675..73096489,2	MCF-7	breast:
2	chr11:73067211..73073171-chr11:73086403..73091347,7	K562	blood:
3	chr11:73065197..73066947-chr11:73090841..73092823,2	K562	blood:
4	chr11:73089858..73092055-chr11:73116123..73118154,2	K562	blood:
5	chr11:72995736..72998591-chr11:73090092..73091920,2	K562	blood:

Variant related genes	Relation type
ENSG00000110237	Chromatin interaction
ENSG00000266866	Chromatin interaction
ENSG00000256448	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1002127	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898917	0.88[EUR][1000 genomes]
rs11544310	1.00[ASN][1000 genomes]
rs11544311	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17244596	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17244602	0.83[AMR][1000 genomes]
rs28400367	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741149	0.84[EUR][1000 genomes]
rs3741151	0.84[EUR][1000 genomes]
rs56742470	0.83[AMR][1000 genomes]
rs57354084	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57893472	0.83[EUR][1000 genomes]
rs58334887	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58564192	0.83[AMR][1000 genomes]
rs60924672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61345051	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592526	0.91[AMR][1000 genomes]
rs7110369	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7112924	1.00[ASN][1000 genomes]
rs7115055	0.83[AMR][1000 genomes]
rs7122825	0.83[EUR][1000 genomes]
rs7129546	0.83[AMR][1000 genomes]
rs7129663	0.84[EUR][1000 genomes]
rs73542929	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542938	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542952	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542960	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542967	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542976	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542979	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542990	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73543000	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73544710	0.85[EUR][1000 genomes]
rs73544711	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73544716	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73544720	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73544729	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73544767	0.91[AMR][1000 genomes]
rs73544783	0.83[AMR][1000 genomes]
rs7925226	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930880	0.83[EUR][1000 genomes]
rs7941454	0.90[EUR][1000 genomes]
rs7951072	0.83[AMR][1000 genomes]
rs7951174	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821041	chr11:72937162-73113080	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv825993	chr11:73029209-73091929	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv897911	chr11:73044351-73108276	Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12099129	ARHGEF17	cis	Whole Blood	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73087800-73095200	Enhancers	Fetal Heart	heart
2	chr11:73088400-73092400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr11:73088400-73093400	Weak transcription	Gastric	stomach
4	chr11:73088400-73100200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr11:73088600-73092600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:73088600-73093400	Weak transcription	Small Intestine	intestine
7	chr11:73088600-73094000	Weak transcription	Fetal Lung	lung
8	chr11:73088600-73100800	Enhancers	Placenta	Placenta
9	chr11:73088800-73092000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:73088800-73093400	Enhancers	Right Ventricle	heart
11	chr11:73088800-73093600	Weak transcription	Fetal Intestine Small	intestine
12	chr11:73088800-73094000	Weak transcription	Fetal Brain Female	brain
13	chr11:73088800-73094000	Weak transcription	HSMM	muscle
14	chr11:73088800-73097800	Enhancers	Psoas Muscle	Psoas
15	chr11:73089000-73092800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:73089000-73093400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr11:73089000-73093600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:73089000-73093600	Weak transcription	HUVEC	blood vessel
19	chr11:73089000-73094000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:73089000-73094000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:73089000-73094000	Weak transcription	Fetal Brain Male	brain
22	chr11:73089000-73094200	Weak transcription	NH-A	brain
23	chr11:73089000-73094200	Weak transcription	NHDF-Ad	bronchial
24	chr11:73089000-73095000	Weak transcription	NHLF	lung
25	chr11:73089000-73096000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr11:73089000-73099600	Enhancers	A549	lung
27	chr11:73089000-73100600	Enhancers	Fetal Muscle Leg	muscle
28	chr11:73089000-73101000	Enhancers	Brain Hippocampus Middle	brain
29	chr11:73089200-73092600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:73089200-73093600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:73089200-73093600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:73089200-73093800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:73089200-73094000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:73089200-73094800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:73089200-73095600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:73089200-73096400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:73089200-73096600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr11:73089200-73097200	Weak transcription	HMEC	breast
39	chr11:73089200-73097800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:73089400-73091600	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr11:73089400-73093200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr11:73089400-73093200	Weak transcription	Thymus	Thymus
43	chr11:73089400-73093800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:73089400-73096600	Enhancers	Primary hematopoietic stem cells	blood
45	chr11:73089600-73095000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:73089600-73096800	Weak transcription	Osteobl	bone
47	chr11:73089800-73091400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr11:73089800-73092000	Genic enhancers	Spleen	Spleen
49	chr11:73089800-73093600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr11:73089800-73094000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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