Variant report

Variant	rs73542960
Chromosome Location	chr11:73115946-73115947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:73115701-73116511	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:73115942-73116461	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:73112653..73117037-chr11:73375086..73378284,4	MCF-7	breast:
2	chr11:73113711..73116580-chr11:73369932..73372135,2	MCF-7	breast:
3	chr11:73111799..73116221-chr11:73117237..73120913,5	K562	blood:

Variant related genes	Relation type
ENSG00000256448	TF binding region
ENSG00000021300	Chromatin interaction
ENSG00000252732	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1002127	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11544310	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11544311	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12099129	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12288753	0.84[EUR][1000 genomes]
rs12290623	0.83[EUR][1000 genomes]
rs17244596	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17244602	0.83[AMR][1000 genomes]
rs17851510	0.87[EUR][1000 genomes]
rs1938777	0.80[EUR][1000 genomes]
rs2298469	0.84[EUR][1000 genomes]
rs28400367	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56742470	1.00[AMR][1000 genomes]
rs57354084	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58334887	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58564192	0.83[AMR][1000 genomes]
rs60924672	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61345051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592526	0.91[AMR][1000 genomes]
rs7110369	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7112924	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114009	0.83[EUR][1000 genomes]
rs7115055	0.83[AMR][1000 genomes]
rs7118982	0.84[EUR][1000 genomes]
rs7129546	1.00[AMR][1000 genomes]
rs7129990	0.83[EUR][1000 genomes]
rs73542929	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542938	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542952	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542967	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542990	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73543000	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73544710	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73544711	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73544716	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73544720	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73544729	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73544767	0.91[AMR][1000 genomes]
rs73544783	0.83[AMR][1000 genomes]
rs7925226	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941454	0.82[EUR][1000 genomes]
rs7951072	0.83[AMR][1000 genomes]
rs7951174	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73542960	ARHGEF17	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73095200-73116200	Weak transcription	Liver	Liver
2	chr11:73096200-73130200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:73097200-73117600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr11:73098600-73126000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:73098600-73132400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:73099200-73139800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr11:73099200-73141000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr11:73099600-73119200	Weak transcription	Fetal Lung	lung
9	chr11:73100000-73116600	Weak transcription	Pancreas	Pancrea
10	chr11:73100000-73118400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr11:73100200-73117400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:73100600-73118600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr11:73101000-73116200	Weak transcription	Brain Angular Gyrus	brain
14	chr11:73101000-73116400	Weak transcription	Brain Substantia Nigra	brain
15	chr11:73101200-73124800	Weak transcription	Psoas Muscle	Psoas
16	chr11:73103600-73118400	Weak transcription	Esophagus	oesophagus
17	chr11:73103800-73116600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:73104000-73116200	Weak transcription	Brain Anterior Caudate	brain
19	chr11:73104600-73123400	Strong transcription	Fetal Stomach	stomach
20	chr11:73104800-73122600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:73105200-73116400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:73105200-73116800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:73105600-73116000	Weak transcription	Colonic Mucosa	Colon
24	chr11:73105800-73116600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr11:73106200-73116400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:73106400-73116600	Weak transcription	Gastric	stomach
27	chr11:73106400-73120200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr11:73107200-73116200	Weak transcription	Lung	lung
29	chr11:73107800-73116200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:73107800-73117600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:73108200-73116200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:73108400-73116400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr11:73109200-73116000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:73109200-73116000	Weak transcription	Placenta	Placenta
35	chr11:73109800-73116200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr11:73110000-73120000	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:73110200-73116000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:73110200-73116000	Weak transcription	Dnd41	blood
39	chr11:73110200-73116600	Weak transcription	Right Ventricle	heart
40	chr11:73110400-73116200	Weak transcription	Left Ventricle	heart
41	chr11:73110400-73116600	Weak transcription	NHEK	skin
42	chr11:73110600-73116400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr11:73110600-73121600	Weak transcription	NHDF-Ad	bronchial
44	chr11:73110600-73123200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr11:73110800-73116000	Weak transcription	NHLF	lung
46	chr11:73110800-73116200	Weak transcription	Fetal Intestine Large	intestine
47	chr11:73110800-73116400	Weak transcription	HSMM	muscle
48	chr11:73110800-73123000	Weak transcription	HUVEC	blood vessel
49	chr11:73110800-73123200	Weak transcription	NH-A	brain
50	chr11:73110800-73124000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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